Bioconductor Software Packages
Bioconductor version: Development (3.20)
Package | Maintainer | Title |
---|---|---|
a4 | Laure Cougnaud | Automated Affymetrix Array Analysis Umbrella Package |
a4Base | Laure Cougnaud | Automated Affymetrix Array Analysis Base Package |
a4Classif | Laure Cougnaud | Automated Affymetrix Array Analysis Classification Package |
a4Core | Laure Cougnaud | Automated Affymetrix Array Analysis Core Package |
a4Preproc | Laure Cougnaud | Automated Affymetrix Array Analysis Preprocessing Package |
a4Reporting | Laure Cougnaud | Automated Affymetrix Array Analysis Reporting Package |
ABarray | Yongming Andrew Sun | Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Microrarray (AB1700) gene expression data. |
abseqR | JiaHong Fong | Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries |
ABSSeq | Wentao Yang | ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences |
acde | Juan Pablo Acosta | Artificial Components Detection of Differentially Expressed Genes |
ACE | Jos B Poell | Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing |
aCGH | Peter Dimitrov | Classes and functions for Array Comparative Genomic Hybridization data |
ACME | Sean Davis | Algorithms for Calculating Microarray Enrichment (ACME) |
ADaCGH2 | Ramon Diaz-Uriarte | Analysis of big data from aCGH experiments using parallel computing and ff objects |
ADAM | Jose Luiz Rybarczyk Filho | ADAM: Activity and Diversity Analysis Module |
ADAMgui | Jose Luiz Rybarczyk Filho | Activity and Diversity Analysis Module Graphical User Interface |
adductomicsR | Josie Hayes | Processing of adductomic mass spectral datasets |
ADImpute | Ana Carolina Leote | Adaptive Dropout Imputer (ADImpute) |
adSplit | Claudio Lottaz | Annotation-Driven Clustering |
adverSCarial | Ghislain FIEVET | adverSCarial, generate and analyze the vulnerability of scRNA-seq classifier to adversarial attacks |
AffiXcan | Alessandro Lussana | A Functional Approach To Impute Genetically Regulated Expression |
affxparser | Kasper Daniel Hansen | Affymetrix File Parsing SDK |
affy | Robert D. Shear | Methods for Affymetrix Oligonucleotide Arrays |
affycomp | Robert D. Shear | Graphics Toolbox for Assessment of Affymetrix Expression Measures |
affyContam | V. Carey | structured corruption of affymetrix cel file data |
affycoretools | James W. MacDonald | Functions useful for those doing repetitive analyses with Affymetrix GeneChips |
affyILM | Myriam Kroll and Fabrice Berger | Linear Model of background subtraction and the Langmuir isotherm |
affyio | Ben Bolstad | Tools for parsing Affymetrix data files |
affylmGUI | Gordon Smyth | GUI for limma Package with Affymetrix Microarrays |
affyPLM | Ben Bolstad | Methods for fitting probe-level models |
AffyRNADegradation | Mario Fasold | Analyze and correct probe positional bias in microarray data due to RNA degradation |
AGDEX | Cuilan lani Gao | Agreement of Differential Expression Analysis |
aggregateBioVar | Jason Ratcliff | Differential Gene Expression Analysis for Multi-subject scRNA-seq |
agilp | Benny Chain | Agilent expression array processing package |
AgiMicroRna | Pedro Lopez-Romero | Processing and Differential Expression Analysis of Agilent microRNA chips |
AHMassBank | Johannes Rainer | MassBank Annotation Resources for AnnotationHub |
AIMS | Eric R Paquet | AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype |
airpart | Wancen Mu | Differential cell-type-specific allelic imbalance |
alabaster | Aaron Lun | Umbrella for the Alabaster Framework |
alabaster.base | Aaron Lun | Save Bioconductor Objects To File |
alabaster.bumpy | Aaron Lun | Save and Load BumpyMatrices to/from file |
alabaster.files | Aaron Lun | Wrappers to Save Common File Formats |
alabaster.mae | Aaron Lun | Load and Save MultiAssayExperiments |
alabaster.matrix | Aaron Lun | Load and Save Artifacts from File |
alabaster.ranges | Aaron Lun | Load and Save Ranges-related Artifacts from File |
alabaster.sce | Aaron Lun | Load and Save SingleCellExperiment from File |
alabaster.schemas | Aaron Lun | Schemas for the Alabaster Framework |
alabaster.se | Aaron Lun | Load and Save SummarizedExperiments from File |
alabaster.spatial | Aaron Lun | Save and Load Spatial 'Omics Data to/from File |
alabaster.string | Aaron Lun | Save and Load Biostrings to/from File |
alabaster.vcf | Aaron Lun | Save and Load Variant Data to/from File |
ALDEx2 | Greg Gloor | Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account |
alevinQC | Charlotte Soneson | Generate QC Reports For Alevin Output |
AllelicImbalance | Jesper R Gadin | Investigates Allele Specific Expression |
AlphaBeta | Yadollah Shahryary Dizaji | Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants |
AlphaMissenseR | Martin Morgan | Accessing AlphaMissense Data Resources in R |
AlpsNMR | Sergio Oller Moreno | Automated spectraL Processing System for NMR |
altcdfenvs | Laurent Gautier | alternative CDF environments (aka probeset mappings) |
AMARETTO | Olivier Gevaert | Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression |
AMOUNTAIN | Dong Li | Active modules for multilayer weighted gene co-expression networks: a continuous optimization approach |
amplican | Eivind Valen | Automated analysis of CRISPR experiments |
Anaquin | Ted Wong | Statistical analysis of sequins |
ANCOMBC | Huang Lin | Microbiome differential abudance and correlation analyses with bias correction |
AneuFinder | Aaron Taudt | Analysis of Copy Number Variation in Single-Cell-Sequencing Data |
ANF | Tianle Ma | Affinity Network Fusion for Complex Patient Clustering |
animalcules | Jessica McClintock | Interactive microbiome analysis toolkit |
annaffy | Colin A. Smith | Annotation tools for Affymetrix biological metadata |
annmap | Chris Wirth | Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis. |
annotate | Bioconductor Package Maintainer | Annotation for microarrays |
AnnotationDbi | Bioconductor Package Maintainer | Manipulation of SQLite-based annotations in Bioconductor |
AnnotationFilter | Bioconductor Package Maintainer | Facilities for Filtering Bioconductor Annotation Resources |
AnnotationForge | Bioconductor Package Maintainer | Tools for building SQLite-based annotation data packages |
AnnotationHub | Bioconductor Package Maintainer | Client to access AnnotationHub resources |
AnnotationHubData | Bioconductor Package Maintainer | Transform public data resources into Bioconductor Data Structures |
annotationTools | Alexandre Kuhn | Annotate microarrays and perform cross-species gene expression analyses using flat file databases |
annotatr | Raymond G. Cavalcante | Annotation of Genomic Regions to Genomic Annotations |
anota | Ola Larsson | ANalysis Of Translational Activity (ANOTA). |
anota2seq | Christian Oertlin, Ola Larsson | Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq |
antiProfiles | Hector Corrada Bravo | Implementation of gene expression anti-profiles |
AnVIL | Marcel Ramos | Bioconductor on the AnVIL compute environment |
AnVILAz | Marcel Ramos | R / Bioconductor Support for the AnVIL Azure Platform |
AnVILBase | Marcel Ramos | Generic functions for interacting with the AnVIL ecosystem |
AnVILBilling | Vince Carey | Provide functions to retrieve and report on usage expenses in NHGRI AnVIL (anvilproject.org). |
AnVILGCP | Marcel Ramos | The GCP R Client for the AnVIL |
AnVILPublish | Marcel Ramos | Publish Packages and Other Resources to AnVIL Workspaces |
AnVILWorkflow | Sehyun Oh | Run workflows implemented in Terra/AnVIL workspace |
APAlyzer | Ruijia Wang | A toolkit for APA analysis using RNA-seq data |
apComplex | Denise Scholtens | Estimate protein complex membership using AP-MS protein data |
apeglm | Anqi Zhu | Approximate posterior estimation for GLM coefficients |
APL | Clemens Kohl | Association Plots |
appreci8R | Sarah Sandmann | appreci8R: an R/Bioconductor package for filtering SNVs and short indels with high sensitivity and high PPV |
aroma.light | Henrik Bengtsson | Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types |
ArrayExpress | Jose Marugan | Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet |
arrayMvout | V. Carey | multivariate outlier detection for expression array QA |
arrayQuality | Agnes Paquet | Assessing array quality on spotted arrays |
arrayQualityMetrics | Mike Smith | Quality metrics report for microarray data sets |
ARRmNormalization | Jean-Philippe Fortin | Adaptive Robust Regression normalization for Illumina methylation data |
artMS | David Jimenez-Morales | Analytical R tools for Mass Spectrometry |
ASAFE | Qian Zhang | Ancestry Specific Allele Frequency Estimation |
ASEB | Likun Wang | Predict Acetylated Lysine Sites |
ASGSCA | Hela Romdhani | Association Studies for multiple SNPs and multiple traits using Generalized Structured Equation Models |
ASICS | Gaëlle Lefort | Automatic Statistical Identification in Complex Spectra |
ASpli | Ariel Chernomoretz | Analysis of Alternative Splicing Using RNA-Seq |
AssessORF | Deepank Korandla | Assess Gene Predictions Using Proteomics and Evolutionary Conservation |
ASSET | Samsiddhi Bhattacharjee | An R package for subset-based association analysis of heterogeneous traits and subtypes |
ASSIGN | Ying Shen, W. Evan Johnson, David Jenkins, Mumtehena Rahman | Adaptive Signature Selection and InteGratioN (ASSIGN) |
assorthead | Aaron Lun | Assorted Header-Only C++ Libraries |
ASURAT | Keita Iida | Functional annotation-driven unsupervised clustering for single-cell data |
ATACCoGAPS | Rossin Erbe | Analysis Tools for scATACseq Data with CoGAPS |
ATACseqQC | Jianhong Ou | ATAC-seq Quality Control |
ATACseqTFEA | Jianhong Ou | Transcription Factor Enrichment Analysis for ATAC-seq |
atena | Robert Castelo | Analysis of Transposable Elements |
atSNP | Sunyoung Shin | Affinity test for identifying regulatory SNPs |
attract | Samuel Zimmerman | Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape |
AUCell | Gert Hulselmans | AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures) |
autonomics | Aditya Bhagwat | Unified statistal Modeling of Omics Data |
AWFisher | Zhiguang Huo | An R package for fast computing for adaptively weighted fisher's method |
awst | Davide Risso | Asymmetric Within-Sample Transformation |
BaalChIP | Ines de Santiago | BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes |
bacon | Maarten van Iterson | Controlling bias and inflation in association studies using the empirical null distribution |
BADER | Andreas Neudecker | Bayesian Analysis of Differential Expression in RNA Sequencing Data |
BadRegionFinder | Sarah Sandmann | BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage |
BAGS | Alejandro Quiroz-Zarate | A Bayesian Approach for Geneset Selection |
ballgown | Jack Fu | Flexible, isoform-level differential expression analysis |
bambu | Ying Chen | Context-Aware Transcript Quantification from Long Read RNA-Seq data |
bamsignals | Johannes Helmuth | Extract read count signals from bam files |
BANDITS | Simone Tiberi | BANDITS: Bayesian ANalysis of DIfferenTial Splicing |
bandle | Oliver M. Crook | An R package for the Bayesian analysis of differential subcellular localisation experiments |
Banksy | Joseph Lee | Spatial transcriptomic clustering |
banocc | George Weingart, Curtis Huttenhower | Bayesian ANalysis Of Compositional Covariance |
barcodetrackR | Diego Alexander Espinoza | Functions for Analyzing Cellular Barcoding Data |
basecallQC | Thomas Carroll | Working with Illumina Basecalling and Demultiplexing input and output files |
BaseSpaceR | Jared O'Connell | R SDK for BaseSpace RESTful API |
Basic4Cseq | Carolin Walter | Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data |
BASiCS | Catalina Vallejos | Bayesian Analysis of Single-Cell Sequencing data |
BASiCStan | Alan O'Callaghan | Stan implementation of BASiCS |
BasicSTARRseq | Annika Buerger | Basic peak calling on STARR-seq data |
basilisk | Aaron Lun | Freezing Python Dependencies Inside Bioconductor Packages |
basilisk.utils | Aaron Lun | Basilisk Installation Utilities |
batchelor | Aaron Lun | Single-Cell Batch Correction Methods |
BatchQC | Jessica McClintock | Batch Effects Quality Control Software |
BayesKnockdown | William Chad Young | BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data |
BayesSpace | Matt Stone | Clustering and Resolution Enhancement of Spatial Transcriptomes |
bayNorm | Wenhao Tang | Single-cell RNA sequencing data normalization |
baySeq | Samuel Granjeaud | Empirical Bayesian analysis of patterns of differential expression in count data |
BBCAnalyzer | Sarah Sandmann | BBCAnalyzer: an R/Bioconductor package for visualizing base counts |
BCRANK | Adam Ameur | Predicting binding site consensus from ranked DNA sequences |
bcSeq | Jiaxing Lin | Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens |
beachmat | Aaron Lun | Compiling Bioconductor to Handle Each Matrix Type |
beachmat.hdf5 | Aaron Lun | beachmat bindings for HDF5-backed matrices |
beadarray | Mark Dunning | Quality assessment and low-level analysis for Illumina BeadArray data |
BeadDataPackR | Mike Smith | Compression of Illumina BeadArray data |
BEARscc | Benjamin Schuster-Boeckler | BEARscc (Bayesian ERCC Assesstment of Robustness of Single Cell Clusters) |
BEAT | Kemal Akman | BEAT - BS-Seq Epimutation Analysis Toolkit |
BEclear | Livia Rasp | Correction of batch effects in DNA methylation data |
beer | Athena Chen | Bayesian Enrichment Estimation in R |
benchdamic | Matteo Calgaro | Benchmark of differential abundance methods on microbiome data |
BERT | Yannis Schumann | High Performance Data Integration for Large-Scale Analyses of Incomplete Omic Profiles Using Batch-Effect Reduction Trees (BERT) |
betaHMM | Koyel Majumdar | A Hidden Markov Model Approach for Identifying Differentially Methylated Sites and Regions for Beta-Valued DNA Methylation Data |
bettr | Charlotte Soneson | A Better Way To Explore What Is Best |
BG2 | Jacob Williams | Performs Bayesian GWAS analysis for non-Gaussian data using BG2 |
BgeeCall | Julien Wollbrett | Automatic RNA-Seq present/absent gene expression calls generation |
BgeeDB | Julien Wollbrett, Julien Roux, Andrea Komljenovic, Frederic Bastian | Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology |
bgx | Ernest Turro | Bayesian Gene eXpression |
BicARE | Pierre Gestraud | Biclustering Analysis and Results Exploration |
BiFET | Ahrim Youn | Bias-free Footprint Enrichment Test |
BiGGR | Anand K. Gavai, Hannes Hettling | Constraint based modeling in R using metabolic reconstruction databases |
bigmelon | Leonard C. Schalkwyk | Illumina methylation array analysis for large experiments |
BindingSiteFinder | Mirko Brüggemann | Binding site defintion based on iCLIP data |
bioassayR | Daniela Cassol | Cross-target analysis of small molecule bioactivity |
Biobase | Bioconductor Package Maintainer | Biobase: Base functions for Bioconductor |
biobroom | John D. Storey and Andrew J. Bass | Turn Bioconductor objects into tidy data frames |
biobtreeR | Tamer Gur | Using biobtree tool from R |
bioCancer | Karim Mezhoud | Interactive Multi-Omics Cancers Data Visualization and Analysis |
BioCartaImage | Zuguang Gu | BioCarta Pathway Images |
BiocBaseUtils | Marcel Ramos | General utility functions for developing Bioconductor packages |
BiocBook | Jacques Serizay | Write, containerize, publish and version Quarto books with Bioconductor |
BiocCheck | Marcel Ramos | Bioconductor-specific package checks |
BiocFHIR | Vincent Carey | Illustration of FHIR ingestion and transformation using R |
BiocFileCache | Lori Shepherd | Manage Files Across Sessions |
BiocGenerics | Hervé Pagès | S4 generic functions used in Bioconductor |
biocGraph | Florian Hahne | Graph examples and use cases in Bioinformatics |
BiocHail | Vincent Carey | basilisk and hail |
BiocHubsShiny | Marcel Ramos | View AnnotationHub and ExperimentHub Resources Interactively |
BiocIO | Marcel Ramos | Standard Input and Output for Bioconductor Packages |
BiocNeighbors | Aaron Lun | Nearest Neighbor Detection for Bioconductor Packages |
BiocOncoTK | VJ Carey | Bioconductor components for general cancer genomics |
BioCor | Lluís Revilla Sancho | Functional similarities |
BiocParallel | Martin Morgan | Bioconductor facilities for parallel evaluation |
BiocPkgTools | Sean Davis | Collection of simple tools for learning about Bioconductor Packages |
biocroxytest | Francesc Catala-Moll | Handle Long Tests in Bioconductor Packages |
BiocSet | Kayla Morrell | Representing Different Biological Sets |
BiocSingular | Aaron Lun | Singular Value Decomposition for Bioconductor Packages |
BiocSklearn | Vince Carey | interface to python sklearn via Rstudio reticulate |
BiocStyle | Bioconductor Package | Standard styles for vignettes and other Bioconductor documents |
biocthis | Leonardo Collado-Torres | Automate package and project setup for Bioconductor packages |
BiocVersion | Bioconductor Package Maintainer | Set the appropriate version of Bioconductor packages |
biocViews | Bioconductor Package Maintainer | Categorized views of R package repositories |
BiocWorkflowTools | Mike Smith | Tools to aid the development of Bioconductor Workflow packages |
biodb | Pierrick Roger | biodb, a library and a development framework for connecting to chemical and biological databases |
biodbChebi | Pierrick Roger | biodbChebi, a library for connecting to the ChEBI Database |
biodbExpasy | Pierrick Roger | biodbExpasy, a library for connecting to Expasy ENZYME database. |
biodbHmdb | Pierrick Roger | biodbHmdb, a library for connecting to the HMDB Database |
biodbKegg | Pierrick Roger | biodbKegg, a library for connecting to the KEGG Database |
biodbNcbi | Pierrick Roger | biodbNcbi, a library for connecting to NCBI Databases. |
biodbNci | Pierrick Roger | biodbNci, a library for connecting to biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database |
biodbUniprot | Pierrick Roger | biodbUniprot, a library for connecting to the Uniprot Database |
bioDist | Bioconductor Package Maintainer | Different distance measures |
BioGA | Dany Mukesha | Bioinformatics Genetic Algorithm (BioGA) |
biomaRt | Mike Smith | Interface to BioMart databases (i.e. Ensembl) |
biomformat | Paul J. McMurdie | An interface package for the BIOM file format |
BioMVCClass | Elizabeth Whalen | Model-View-Controller (MVC) Classes That Use Biobase |
biomvRCNS | Yang Du | Copy Number study and Segmentation for multivariate biological data |
BioNAR | Anatoly Sorokin | Biological Network Analysis in R |
BioNERO | Fabricio Almeida-Silva | Biological Network Reconstruction Omnibus |
BioNet | Marcus Dittrich | Routines for the functional analysis of biological networks |
BioQC | Jitao David Zhang | Detect tissue heterogeneity in expression profiles with gene sets |
biosigner | Etienne A. Thevenot | Signature discovery from omics data |
Biostrings | Hervé Pagès | Efficient manipulation of biological strings |
BioTIP | Yuxi (Jennifer) Sun, Zhezhen Wang, and X Holly Yang | BioTIP: An R package for characterization of Biological Tipping-Point |
biotmle | Nima Hejazi | Targeted Learning with Moderated Statistics for Biomarker Discovery |
biovizBase | Michael Lawrence | Basic graphic utilities for visualization of genomic data. |
BiRewire | Andrea Gobbi | High-performing routines for the randomization of a bipartite graph (or a binary event matrix), undirected and directed signed graph preserving degree distribution (or marginal totals) |
biscuiteer | Jacob Morrison | Convenience Functions for Biscuit |
BiSeq | Katja Hebestreit | Processing and analyzing bisulfite sequencing data |
blacksheepr | RugglesLab | Outlier Analysis for pairwise differential comparison |
blima | Vojtěch Kulvait | Tools for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level |
BLMA | Van-Dung Pham | BLMA: A package for bi-level meta-analysis |
BloodGen3Module | Darawan Rinchai | This R package for performing module repertoire analyses and generating fingerprint representations |
bluster | Aaron Lun | Clustering Algorithms for Bioconductor |
bnbc | Kipper Fletez-Brant | Bandwise normalization and batch correction of Hi-C data |
bnem | Martin Pirkl | Training of logical models from indirect measurements of perturbation experiments |
BOBaFIT | Gaia Mazzocchetti | Refitting diploid region profiles using a clustering procedure |
borealis | Garrett Jenkinson | Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution |
BPRMeth | Chantriolnt-Andreas Kapourani | Model higher-order methylation profiles |
BRAIN | Piotr Dittwald | Baffling Recursive Algorithm for Isotope distributioN calculations |
brainflowprobes | Amanda Price | Plots and annotation for choosing BrainFlow target probe sequence |
branchpointer | Beth Signal | Prediction of intronic splicing branchpoints |
breakpointR | David Porubsky | Find breakpoints in Strand-seq data |
brendaDb | Yi Zhou | The BRENDA Enzyme Database |
BREW3R.r | Lucille Lopez-Delisle | R package associated to BREW3R |
BRGenomics | Mike DeBerardine | Tools for the Efficient Analysis of High-Resolution Genomics Data |
BridgeDbR | Egon Willighagen | Code for using BridgeDb identifier mapping framework from within R |
broadSeq | Rishi Das Roy | broadSeq : for streamlined exploration of RNA-seq data |
BrowserViz | Arkadiusz Gladki | BrowserViz: interactive R/browser graphics using websockets and JSON |
BSgenome | Hervé Pagès | Software infrastructure for efficient representation of full genomes and their SNPs |
BSgenomeForge | Hervé Pagès | Forge BSgenome data packages |
bsseq | Kasper Daniel Hansen | Analyze, manage and store bisulfite sequencing data |
BubbleTree | Todd Creasy, Wei Zhu | BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing data |
BufferedMatrix | Ben Bolstad | A matrix data storage object held in temporary files |
BufferedMatrixMethods | Ben Bolstad | Microarray Data related methods that utlize BufferedMatrix objects |
bugsigdbr | Ludwig Geistlinger | R-side access to published microbial signatures from BugSigDB |
BUMHMM | Alina Selega | Computational pipeline for computing probability of modification from structure probing experiment data |
bumphunter | Tamilselvi Guharaj | Bump Hunter |
BumpyMatrix | Aaron Lun | Bumpy Matrix of Non-Scalar Objects |
BUS | Yuanhua Liu | Gene network reconstruction |
BUScorrect | Xiangyu Luo | Batch Effects Correction with Unknown Subtypes |
BUSpaRse | Lambda Moses | kallisto | bustools R utilities |
BUSseq | Fangda Song | Batch Effect Correction with Unknow Subtypes for scRNA-seq data |
CaDrA | Reina Chau | Candidate Driver Analysis |
CAEN | Zhou Yan | Category encoding method for selecting feature genes for the classification of single-cell RNA-seq |
CAFE | Sander Bollen | Chromosmal Aberrations Finder in Expression data |
CAGEfightR | Malte Thodberg | Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor |
cageminer | Fabrício Almeida-Silva | Candidate Gene Miner |
CAGEr | Charles Plessy | Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining |
calm | Kun Liang | Covariate Assisted Large-scale Multiple testing |
CAMERA | Steffen Neumann | Collection of annotation related methods for mass spectrometry data |
CaMutQC | Xin Wang | An R Package for Comprehensive Filtration and Selection of Cancer Somatic Mutations |
canceR | Karim Mezhoud | A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC |
cancerclass | Daniel Kosztyla | Development and validation of diagnostic tests from high-dimensional molecular data |
cardelino | Davis McCarthy | Clone Identification from Single Cell Data |
Cardinal | Kylie Ariel Bemis | A mass spectrometry imaging toolbox for statistical analysis |
CardinalIO | Kylie Ariel Bemis | Read and write mass spectrometry imaging files |
CARNIVAL | Attila Gabor | A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming |
casper | David Rossell | Characterization of Alternative Splicing based on Paired-End Reads |
CATALYST | Helena L. Crowell | Cytometry dATa anALYSis Tools |
Category | Bioconductor Package Maintainer | Category Analysis |
categoryCompare | Robert M. Flight | Meta-analysis of high-throughput experiments using feature annotations |
CatsCradle | Michael Shapiro | This package provides methods for analysing spatial transcriptomics data and for discovering gene clusters |
CausalR | Glyn Bradley, Steven Barrett | Causal network analysis methods |
cbaf | Arman Shahrisa | Automated functions for comparing various omic data from cbioportal.org |
CBEA | Quang Nguyen | Competitive Balances for Taxonomic Enrichment Analysis in R |
cBioPortalData | Marcel Ramos | Exposes and Makes Available Data from the cBioPortal Web Resources |
CBNplot | Noriaki Sato | plot bayesian network inferred from gene expression data based on enrichment analysis results |
cbpManager | Arsenij Ustjanzew | Generate, manage, and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics |
ccfindR | Jun Woo | Cancer Clone Finder |
ccImpute | Marcin Malec | ccImpute: an accurate and scalable consensus clustering based approach to impute dropout events in the single-cell RNA-seq data (https://doi.org/10.1186/s12859-022-04814-8) |
ccmap | Alex Pickering | Combination Connectivity Mapping |
CCPlotR | Sarah Ennis | Plots For Visualising Cell-Cell Interactions |
CCPROMISE | Xueyuan Cao | PROMISE analysis with Canonical Correlation for Two Forms of High Dimensional Genetic Data |
ccrepe | Emma Schwager,Craig Bielski, George Weingart | ccrepe_and_nc.score |
CDI | Jiyuan Fang | Clustering Deviation Index (CDI) |
celaref | Sarah Williams | Single-cell RNAseq cell cluster labelling by reference |
celda | Joshua Campbell | CEllular Latent Dirichlet Allocation |
CellaRepertorium | Andrew McDavid | Data structures, clustering and testing for single cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq) |
CellBarcode | Wenjie Sun | Cellular DNA Barcode Analysis toolkit |
cellbaseR | Mohammed OE Abdallah | Querying annotation data from the high performance Cellbase web |
CellBench | Shian Su | Construct Benchmarks for Single Cell Analysis Methods |
CelliD | Akira Cortal | Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis |
cellity | Tomislav Ilicic | Quality Control for Single-Cell RNA-seq Data |
CellMapper | Brad Nelms | Predict genes expressed selectively in specific cell types |
cellmigRation | Waldir Leoncio | Track Cells, Analyze Cell Trajectories and Compute Migration Statistics |
CellMixS | Almut Lütge | Evaluate Cellspecific Mixing |
CellNOptR | Attila Gabor | Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data |
cellscape | Shixiang Wang | Explores single cell copy number profiles in the context of a single cell tree |
CellScore | Nancy Mah | Tool for Evaluation of Cell Identity from Transcription Profiles |
CellTrails | Daniel Ellwanger | Reconstruction, visualization and analysis of branching trajectories |
cellxgenedp | Martin Morgan | Discover and Access Single Cell Data Sets in the CELLxGENE Data Portal |
CEMiTool | Helder Nakaya | Co-expression Modules identification Tool |
censcyt | Reto Gerber | Differential abundance analysis with a right censored covariate in high-dimensional cytometry |
Cepo | Hani Jieun Kim | Cepo for the identification of differentially stable genes |
ceRNAnetsim | Selcen Ari Yuka | Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA) |
CeTF | Carlos Alberto Oliveira de Biagi Junior | Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis |
CexoR | Pedro Madrigal | An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates |
CFAssay | Herbert Braselmann | Statistical analysis for the Colony Formation Assay |
cfdnakit | Pitithat Puranachot | Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA) |
cfDNAPro | Haichao Wang | cfDNAPro extracts and Visualises biological features from whole genome sequencing data of cell-free DNA |
cfTools | Ran Hu | Informatics Tools for Cell-Free DNA Study |
CGEN | Justin Lee | An R package for analysis of case-control studies in genetic epidemiology |
CGHbase | Mark van de Wiel | CGHbase: Base functions and classes for arrayCGH data analysis. |
CGHcall | Mark van de Wiel | Calling aberrations for array CGH tumor profiles. |
cghMCR | J. Zhang | Find chromosome regions showing common gains/losses |
CGHnormaliter | Bart P.P. van Houte | Normalization of array CGH data with imbalanced aberrations. |
CGHregions | Sjoerd Vosse | Dimension Reduction for Array CGH Data with Minimal Information Loss. |
ChAMP | Yuan Tian | Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC |
ChemmineOB | Thomas Girke | R interface to a subset of OpenBabel functionalities |
ChemmineR | Thomas Girke | Cheminformatics Toolkit for R |
CHETAH | Jurrian de Kanter | Fast and accurate scRNA-seq cell type identification |
Chicago | Mikhail Spivakov | CHiCAGO: Capture Hi-C Analysis of Genomic Organization |
chihaya | Aaron Lun | Save Delayed Operations to a HDF5 File |
chimeraviz | Stian Lågstad | Visualization tools for gene fusions |
ChIPanalyser | Patrick C.N. Martin | ChIPanalyser: Predicting Transcription Factor Binding Sites |
ChIPComp | Li Chen | Quantitative comparison of multiple ChIP-seq datasets |
chipenrich | Kai Wang | Gene Set Enrichment For ChIP-seq Peak Data |
ChIPexoQual | Rene Welch | ChIPexoQual |
ChIPpeakAnno | Jianhong Ou, Lihua Julie Zhu, Kai Hu, Junhui Li | Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data |
ChIPQC | Tom Carroll, Rory Stark | Quality metrics for ChIPseq data |
ChIPseeker | Guangchuang Yu | ChIPseeker for ChIP peak Annotation, Comparison, and Visualization |
chipseq | Bioconductor Package Maintainer | chipseq: A package for analyzing chipseq data |
ChIPseqR | Peter Humburg | Identifying Protein Binding Sites in High-Throughput Sequencing Data |
ChIPsim | Peter Humburg | Simulation of ChIP-seq experiments |
ChIPXpress | George Wu | ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles |
chopsticks | Hin-Tak Leung | The 'snp.matrix' and 'X.snp.matrix' Classes |
chromDraw | Jan Janecka | chromDraw is a R package for drawing the schemes of karyotypes in the linear and circular fashion. |
ChromHeatMap | Tim F. Rayner | Heat map plotting by genome coordinate |
chromPlot | Karen Y. Orostica | Global visualization tool of genomic data |
ChromSCape | Pacome Prompsy | Analysis of single-cell epigenomics datasets with a Shiny App |
chromstaR | Aaron Taudt | Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data |
chromVAR | Alicia Schep | Chromatin Variation Across Regions |
CHRONOS | Panos Balomenos | CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis |
cicero | Hannah Pliner | Predict cis-co-accessibility from single-cell chromatin accessibility data |
CIMICE | Nicolò Rossi | CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution |
CINdex | Yuriy Gusev | Chromosome Instability Index |
circRNAprofiler | Simona Aufiero | circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs |
CircSeqAlignTk | Jianqiang Sun | A toolkit for end-to-end analysis of RNA-seq data for circular genomes |
cisPath | Likun Wang | Visualization and management of the protein-protein interaction networks. |
CiteFuse | Yingxin Lin | CiteFuse: multi-modal analysis of CITE-seq data |
ClassifyR | Dario Strbenac | A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing |
cleanUpdTSeq | Jianhong Ou ; Lihua Julie Zhu | cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending data |
CleanUpRNAseq | Haibo Liu | Detect and Correct Genomic DNA Contamination in RNA-seq Data |
cleaver | Sebastian Gibb | Cleavage of Polypeptide Sequences |
clevRvis | Sarah Sandmann | Visualization Techniques for Clonal Evolution |
clippda | Stephen Nyangoma | A package for the clinical proteomic profiling data analysis |
clipper | Paolo Martini | Gene Set Analysis Exploiting Pathway Topology |
cliProfiler | You Zhou | A package for the CLIP data visualization |
cliqueMS | Oriol Senan Campos | Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data |
Clomial | Habil Zare | Infers clonal composition of a tumor |
clst | Noah Hoffman | Classification by local similarity threshold |
clstutils | Noah Hoffman | Tools for performing taxonomic assignment |
CluMSID | Tobias Depke | Clustering of MS2 Spectra for Metabolite Identification |
ClustAll | Asier Ortega-Legarreta | ClustAll: Data driven strategy to robustly identify stratification of patients within complex diseases |
clustComp | Aurora Torrente | Clustering Comparison Package |
clusterExperiment | Elizabeth Purdom | Compare Clusterings for Single-Cell Sequencing |
ClusterFoldSimilarity | Oscar Gonzalez-Velasco | Calculate similarity of clusters from different single cell samples using foldchanges |
ClusterJudge | Adrian Pasculescu | Judging Quality of Clustering Methods using Mutual Information |
clusterProfiler | Guangchuang Yu | A universal enrichment tool for interpreting omics data |
clusterSeq | Samuel Granjeaud | Clustering of high-throughput sequencing data by identifying co-expression patterns |
ClusterSignificance | Jason T Serviss | The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data |
clusterStab | James W. MacDonald | Compute cluster stability scores for microarray data |
clustifyr | Rui Fu | Classifier for Single-cell RNA-seq Using Cell Clusters |
ClustIRR | Simo Kitanovski | Clustering of immune receptor repertoires |
CMA | Roman Hornung | Synthesis of microarray-based classification |
cmapR | Ted Natoli | CMap Tools in R |
cn.farms | Andreas Mitterecker | cn.FARMS - factor analysis for copy number estimation |
cn.mops | Gundula Povysil | cn.mops - Mixture of Poissons for CNV detection in NGS data |
CNAnorm | Stefano Berri | A normalization method for Copy Number Aberration in cancer samples |
CNEr | Ge Tan | CNE Detection and Visualization |
CNORdt | A. MacNamara | Add-on to CellNOptR: Discretized time treatments |
CNORfeeder | Attila Gabor | Integration of CellNOptR to add missing links |
CNORfuzzy | T. Cokelaer | Addon to CellNOptR: Fuzzy Logic |
CNORode | Attila Gabor | ODE add-on to CellNOptR |
CNTools | J. Zhang | Convert segment data into a region by sample matrix to allow for other high level computational analyses. |
CNVfilteR | Jose Marcos Moreno-Cabrera | Identifies false positives of CNV calling tools by using SNV calls |
cnvGSA | Joseph Lugo | Gene Set Analysis of (Rare) Copy Number Variants |
CNViz | Rebecca Greenblatt | Copy Number Visualization |
CNVMetrics | Astrid Deschênes | Copy Number Variant Metrics |
CNVPanelizer | Thomas Wolf | Reliable CNV detection in targeted sequencing applications |
CNVRanger | Ludwig Geistlinger | Summarization and expression/phenotype association of CNV ranges |
CNVrd2 | Hoang Tan Nguyen | CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data. |
CoCiteStats | Bioconductor Package Maintainer | Different test statistics based on co-citation. |
COCOA | John Lawson | Coordinate Covariation Analysis |
codelink | Diego Diez | Manipulation of Codelink microarray data |
CODEX | Yuchao Jiang | A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing |
CoGAPS | Elana J. Fertig, Thomas D. Sherman, Jeanette Johnson, Dmitrijs Lvovs | Coordinated Gene Activity in Pattern Sets |
cogena | Zhilong Jia | co-expressed gene-set enrichment analysis |
cogeqc | Fabrício Almeida-Silva | Systematic quality checks on comparative genomics analyses |
Cogito | Annika Bürger | Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic and epigenomic data sets |
coGPS | Yingying Wei | cancer outlier Gene Profile Sets |
cola | Zuguang Gu | A Framework for Consensus Partitioning |
comapr | Ruqian Lyu | Crossover analysis and genetic map construction |
combi | Stijn Hawinkel | Compositional omics model based visual integration |
coMET | Tiphaine Martin | coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns |
coMethDMR | Fernanda Veitzman | Accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies |
COMPASS | Greg Finak | Combinatorial Polyfunctionality Analysis of Single Cells |
compcodeR | Charlotte Soneson | RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods |
compEpiTools | Mattia Furlan | Tools for computational epigenomics |
ComplexHeatmap | Zuguang Gu | Make Complex Heatmaps |
CompoundDb | Johannes Rainer | Creating and Using (Chemical) Compound Annotation Databases |
ComPrAn | Petra Palenikova | Complexome Profiling Analysis package |
compSPOT | Sydney Grant | compSPOT: Tool for identifying and comparing significantly mutated genomic hotspots |
concordexR | Kayla Jackson | Identify Spatial Homogeneous Regions with concordex |
condiments | Hector Roux de Bezieux | Differential Topology, Progression and Differentiation |
CONFESS | Diana LOW | Cell OrderiNg by FluorEScence Signal |
consensus | Tim Peters | Cross-platform consensus analysis of genomic measurements via interlaboratory testing method |
ConsensusClusterPlus | Matt Wilkerson | ConsensusClusterPlus |
consensusDE | Ashley J. Waardenberg | RNA-seq analysis using multiple algorithms |
consensusOV | Benjamin Haibe-Kains | Gene expression-based subtype classification for high-grade serous ovarian cancer |
consensusSeekeR | Astrid Deschênes | Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges |
consICA | Petr V. Nazarov | consensus Independent Component Analysis |
CONSTANd | Dirk Valkenborg | Data normalization by matrix raking |
conumee | Volker Hovestadt | Enhanced copy-number variation analysis using Illumina DNA methylation arrays |
convert | Yee Hwa (Jean) Yang | Convert Microarray Data Objects |
copa | James W. MacDonald | Functions to perform cancer outlier profile analysis. |
CopyNumberPlots | Bernat Gel | Create Copy-Number Plots using karyoploteR functionality |
coRdon | Anamaria Elek | Codon Usage Analysis and Prediction of Gene Expressivity |
CoreGx | Benjamin Haibe-Kains | Classes and Functions to Serve as the Basis for Other 'Gx' Packages |
Cormotif | Yingying Wei | Correlation Motif Fit |
corral | Lauren Hsu | Correspondence Analysis for Single Cell Data |
coseq | Andrea Rau | Co-Expression Analysis of Sequencing Data |
cosmiq | David Fischer | cosmiq - COmbining Single Masses Into Quantities |
cosmosR | Attila Gabor | COSMOS (Causal Oriented Search of Multi-Omic Space) |
COSNet | Marco Frasca | Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings |
COTAN | Galfrè Silvia Giulia | COexpression Tables ANalysis |
countsimQC | Charlotte Soneson | Compare Characteristic Features of Count Data Sets |
covEB | C. Pacini | Empirical Bayes estimate of block diagonal covariance matrices |
CoverageView | Ernesto Lowy | Coverage visualization package for R |
covRNA | Lara Urban | Multivariate Analysis of Transcriptomic Data |
cpvSNP | Caitlin McHugh | Gene set analysis methods for SNP association p-values that lie in genes in given gene sets |
cqn | Kasper Daniel Hansen | Conditional quantile normalization |
CRImage | Henrik Failmezger, Yinyin Yuan | CRImage a package to classify cells and calculate tumour cellularity |
CRISPRball | Jared Andrews | Shiny Application for Interactive CRISPR Screen Visualization, Exploration, Comparison, and Filtering |
crisprBase | Jean-Philippe Fortin | Base functions and classes for CRISPR gRNA design |
crisprBowtie | Jean-Philippe Fortin | Bowtie-based alignment of CRISPR gRNA spacer sequences |
crisprBwa | Jean-Philippe Fortin | BWA-based alignment of CRISPR gRNA spacer sequences |
crisprDesign | Jean-Philippe Fortin | Comprehensive design of CRISPR gRNAs for nucleases and base editors |
crisprScore | Jean-Philippe Fortin | On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs |
CRISPRseek | Lihua Julie Zhu | Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems |
crisprShiny | Jean-Philippe Fortin | Exploring curated CRISPR gRNAs via Shiny |
CrispRVariants | Helen Lindsay | Tools for counting and visualising mutations in a target location |
crisprVerse | Jean-Philippe Fortin | Easily install and load the crisprVerse ecosystem for CRISPR gRNA design |
crisprViz | Jean-Philippe Fortin | Visualization Functions for CRISPR gRNAs |
crlmm | Benilton S Carvalho, Robert Scharpf, Matt Ritchie | Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays |
crossmeta | Alex Pickering | Cross Platform Meta-Analysis of Microarray Data |
CSAR | Jose M Muino | Statistical tools for the analysis of ChIP-seq data |
csaw | Aaron Lun | ChIP-Seq Analysis with Windows |
csdR | Jakob Peder Pettersen | Differential gene co-expression |
CSSQ | Fan Lab at Georgia Institute of Technology | Chip-seq Signal Quantifier Pipeline |
ctc | Antoine Lucas | Cluster and Tree Conversion. |
CTdata | Laurent Gatto | Data companion to CTexploreR |
CTDquerier | Xavier Escribà-Montagut | Package for CTDbase data query, visualization and downstream analysis |
CTexploreR | Axelle Loriot | Explores Cancer Testis Genes |
cTRAP | Nuno Saraiva-Agostinho | Identification of candidate causal perturbations from differential gene expression data |
ctsGE | Michal Sharabi-Schwager | Clustering of Time Series Gene Expression data |
CTSV | Jinge Yu Developer | Identification of cell-type-specific spatially variable genes accounting for excess zeros |
cummeRbund | Loyal A. Goff | Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data. |
CuratedAtlasQueryR | Stefano Mangiola | Queries the Human Cell Atlas |
customCMPdb | Yuzhu Duan | Customize and Query Compound Annotation Database |
customProDB | Xiaojing Wang Bo Wen | Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search |
cyanoFilter | Oluwafemi Olusoji | Phytoplankton Population Identification using Cell Pigmentation and/or Complexity |
cycle | Matthias Futschik | Significance of periodic expression pattern in time-series data |
cydar | Aaron Lun | Using Mass Cytometry for Differential Abundance Analyses |
cypress | Shilin Yu | Cell-Type-Specific Power Assessment |
CytoDx | Zicheng Hu | Robust prediction of clinical outcomes using cytometry data without cell gating |
CyTOFpower | Anne-Maud Ferreira | Power analysis for CyTOF experiments |
cytofQC | Jill Lundell | Labels normalized cells for CyTOF data and assigns probabilities for each label |
CytoGLMM | Christof Seiler | Conditional Differential Analysis for Flow and Mass Cytometry Experiments |
cytoKernel | Tusharkanti Ghosh | Differential expression using kernel-based score test |
cytolib | Mike Jiang | C++ infrastructure for representing and interacting with the gated cytometry data |
cytomapper | Lasse Meyer | Visualization of highly multiplexed imaging data in R |
CytoMDS | Philippe Hauchamps | Low Dimensions projection of cytometry samples |
cytoMEM | Jonathan Irish | Marker Enrichment Modeling (MEM) |
CytoML | Mike Jiang | A GatingML Interface for Cross Platform Cytometry Data Sharing |
CytoPipeline | Philippe Hauchamps | Automation and visualization of flow cytometry data analysis pipelines |
CytoPipelineGUI | Philippe Hauchamps | GUI's for visualization of flow cytometry data analysis pipelines |
cytoviewer | Lasse Meyer | An interactive multi-channel image viewer for R |
dada2 | Benjamin Callahan | Accurate, high-resolution sample inference from amplicon sequencing data |
dagLogo | Jianhong Ou | dagLogo: a Bioconductor package for visualizing conserved amino acid sequence pattern in groups based on probability theory |
daMA | Jobst Landgrebe | Efficient design and analysis of factorial two-colour microarray data |
DAMEfinder | Stephany Orjuela | Finds DAMEs - Differential Allelicly MEthylated regions |
DaMiRseq | Mattia Chiesa | Data Mining for RNA-seq data: normalization, feature selection and classification |
Damsel | Caitlin Page | Damsel: an end to end analysis of DamID |
DAPAR | Samuel Wieczorek | Tools for the Differential Analysis of Proteins Abundance with R |
dar | Francesc Catala-Moll | Differential Abundance Analysis by Consensus |
DART | Charles Shijie Zheng | Denoising Algorithm based on Relevance network Topology |
dcanr | Dharmesh D. Bhuva | Differential co-expression/association network analysis |
DCATS | Xinyi Lin | Differential Composition Analysis Transformed by a Similarity matrix |
dce | Kim Philipp Jablonski | Pathway Enrichment Based on Differential Causal Effects |
dcGSA | Jiehuan sun | Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles |
ddCt | Jitao David Zhang | The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR) |
ddPCRclust | Benedikt G. Brink | Clustering algorithm for ddPCR data |
dearseq | Boris P. Hejblum | Differential Expression Analysis for RNA-seq data through a robust variance component test |
debCAM | Lulu Chen | Deconvolution by Convex Analysis of Mixtures |
debrowser | Alper Kucukural | Interactive Differential Expresion Analysis Browser |
DECIPHER | Erik Wright | Tools for curating, analyzing, and manipulating biological sequences |
decompTumor2Sig | Rosario M. Piro | Decomposition of individual tumors into mutational signatures by signature refitting |
DeconRNASeq | Ting Gong | Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq data |
decontam | Benjamin Callahan | Identify Contaminants in Marker-gene and Metagenomics Sequencing Data |
decontX | Yuan Yin | Decontamination of single cell genomics data |
deconvR | Irem B. Gündüz | Simulation and Deconvolution of Omic Profiles |
decoupleR | Pau Badia-i-Mompel | decoupleR: Ensemble of computational methods to infer biological activities from omics data |
DeepPINCS | Dongmin Jung | Protein Interactions and Networks with Compounds based on Sequences using Deep Learning |
deepSNV | Moritz Gerstung | Detection of subclonal SNVs in deep sequencing data. |
DeepTarget | Trinh Nguyen | Deep characterization of cancer drugs |
DEFormats | Andrzej Oleś | Differential gene expression data formats converter |
DegCre | Brian S. Roberts | Probabilistic association of DEGs to CREs from differential data |
DegNorm | Ji-Ping Wang | DegNorm: degradation normalization for RNA-seq data |
DEGraph | Laurent Jacob | Two-sample tests on a graph |
DEGreport | Lorena Pantano | Report of DEG analysis |
DEGseq | Likun Wang | Identify Differentially Expressed Genes from RNA-seq data |
DelayedArray | Hervé Pagès | A unified framework for working transparently with on-disk and in-memory array-like datasets |
DelayedDataFrame | Qian Liu | Delayed operation on DataFrame using standard DataFrame metaphor |
DelayedMatrixStats | Peter Hickey | Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects |
DelayedRandomArray | Aaron Lun | Delayed Arrays of Random Values |
DelayedTensor | Koki Tsuyuzaki | R package for sparse and out-of-core arithmetic and decomposition of Tensor |
DELocal | Rishi Das Roy | Identifies differentially expressed genes with respect to other local genes |
deltaCaptureC | Michael Shapiro | This Package Discovers Meso-scale Chromatin Remodeling from 3C Data |
deltaGseg | Diana Low | deltaGseg |
DeMAND | Jung Hoon Woo, Mariano Alvarez | DeMAND |
DeMixT | Ruonan Li | Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms |
demuxmix | Hans-Ulrich Klein | Demultiplexing oligo-barcoded scRNA-seq data using regression mixture models |
demuxSNP | Michael Lynch | scRNAseq demultiplexing using cell hashing and SNPs |
densvis | Alan O'Callaghan | Density-Preserving Data Visualization via Non-Linear Dimensionality Reduction |
DEP | Arne Smits | Differential Enrichment analysis of Proteomics data |
DepecheR | Jakob Theorell | Determination of essential phenotypic elements of clusters in high-dimensional entities |
DepInfeR | Junyan Lu | Inferring tumor-specific cancer dependencies through integrating ex-vivo drug response assays and drug-protein profiling |
DeProViR | Matineh Rahmatbakhsh | A Deep-Learning Framework Based on Pre-trained Sequence Embeddings for Predicting Host-Viral Protein-Protein Interactions |
DEqMS | Yafeng Zhu | a tool to perform statistical analysis of differential protein expression for quantitative proteomics data. |
derfinder | Leonardo Collado-Torres | Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach |
derfinderHelper | Leonardo Collado-Torres | derfinder helper package |
derfinderPlot | Leonardo Collado-Torres | Plotting functions for derfinder |
DEScan2 | Dario Righelli | Differential Enrichment Scan 2 |
DESeq2 | Michael Love | Differential gene expression analysis based on the negative binomial distribution |
DEsingle | Zhun Miao | DEsingle for detecting three types of differential expression in single-cell RNA-seq data |
DESpace | Peiying Cai | DESpace: a framework to discover spatially variable genes |
destiny | Philipp Angerer | Creates diffusion maps |
DEsubs | Aristidis G. Vrahatis, Panos Balomenos | DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments |
DEWSeq | bioinformatics team Hentze | Differential Expressed Windows Based on Negative Binomial Distribution |
DExMA | Juan Antonio Villatoro-García | Differential Expression Meta-Analysis |
DEXSeq | Alejandro Reyes | Inference of differential exon usage in RNA-Seq |
DFP | Rodrigo Alvarez-Glez | Gene Selection |
DIAlignR | Shubham Gupta | Dynamic Programming Based Alignment of MS2 Chromatograms |
DiffBind | Rory Stark | Differential Binding Analysis of ChIP-Seq Peak Data |
diffcoexp | Wenbin Wei | Differential Co-expression Analysis |
diffcyt | Lukas M. Weber | Differential discovery in high-dimensional cytometry via high-resolution clustering |
DifferentialRegulation | Simone Tiberi | Differentially regulated genes from scRNA-seq data |
diffGeneAnalysis | Choudary Jagarlamudi | Performs differential gene expression Analysis |
diffHic | Aaron Lun, Gordon Smyth, Hannah Coughlin | Differential Analysis of Hi-C Data |
DiffLogo | Hendrik Treutler | DiffLogo: A comparative visualisation of biooligomer motifs |
diffuStats | Sergio Picart-Armada | Diffusion scores on biological networks |
diffUTR | Pierre-Luc Germain | diffUTR: Streamlining differential exon and 3' UTR usage |
diggit | Mariano J Alvarez | Inference of Genetic Variants Driving Cellular Phenotypes |
Dino | Jared Brown | Normalization of Single-Cell mRNA Sequencing Data |
dinoR | Michaela Schwaiger | Differential NOMe-seq analysis |
dir.expiry | Aaron Lun | Managing Expiration for Cache Directories |
Director | Katherine Icay | A dynamic visualization tool of multi-level data |
DirichletMultinomial | Martin Morgan | Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data |
discordant | McGrath Max | The Discordant Method: A Novel Approach for Differential Correlation |
DiscoRhythm | Matthew Carlucci | Interactive Workflow for Discovering Rhythmicity in Biological Data |
distinct | Simone Tiberi | distinct: a method for differential analyses via hierarchical permutation tests |
dittoSeq | Daniel Bunis | User Friendly Single-Cell and Bulk RNA Sequencing Visualization |
divergence | Wikum Dinalankara, Luigi Marchionni | Divergence: Functionality for assessing omics data by divergence with respect to a baseline |
dks | Jeffrey T. Leek | The double Kolmogorov-Smirnov package for evaluating multiple testing procedures. |
DMCFB | Farhad Shokoohi | Differentially Methylated Cytosines via a Bayesian Functional Approach |
DMCHMM | Farhad Shokoohi | Differentially Methylated CpG using Hidden Markov Model |
DMRcaller | Nicolae Radu Zabet | Differentially Methylated Regions caller |
DMRcate | Tim Peters | Methylation array and sequencing spatial analysis methods |
DMRScan | Christian M Page | Detection of Differentially Methylated Regions |
dmrseq | Keegan Korthauer | Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing |
DNABarcodeCompatibility | Céline Trébeau | A Tool for Optimizing Combinations of DNA Barcodes Used in Multiplexed Experiments on Next Generation Sequencing Platforms |
DNABarcodes | Tilo Buschmann | A tool for creating and analysing DNA barcodes used in Next Generation Sequencing multiplexing experiments |
DNAcopy | Venkatraman E. Seshan | DNA Copy Number Data Analysis |
DNAfusion | Christoffer Trier Maansson | Identification of gene fusions using paired-end sequencing |
DNAshapeR | Tsu-Pei Chiu | High-throughput prediction of DNA shape features |
DominoEffect | Marija Buljan, Peter Blattmann | Identification and Annotation of Protein Hotspot Residues |
dominoSignal | Jacob T Mitchell | Cell Communication Analysis for Single Cell RNA Sequencing |
doppelgangR | Levi Waldron | Identify likely duplicate samples from genomic or meta-data |
Doscheda | Bruno Contrino | A DownStream Chemo-Proteomics Analysis Pipeline |
DOSE | Guangchuang Yu | Disease Ontology Semantic and Enrichment analysis |
doseR | ake.vastermark | doseR |
doubletrouble | Fabrício Almeida-Silva | Identification and classification of duplicated genes |
drawProteins | Paul Brennan | Package to Draw Protein Schematics from Uniprot API output |
dreamlet | Gabriel Hoffman | Scalable differential expression analysis of single cell transcriptomics datasets with complex study designs |
DRIMSeq | Malgorzata Nowicka | Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq |
DriverNet | Jiarui Ding | Drivernet: uncovering somatic driver mutations modulating transcriptional networks in cancer |
DropletUtils | Jonathan Griffiths | Utilities for Handling Single-Cell Droplet Data |
drugTargetInteractions | Thomas Girke | Drug-Target Interactions |
DrugVsDisease | j. Saez-Rodriguez | Comparison of disease and drug profiles using Gene set Enrichment Analysis |
DSS | Hao Wu, Hao Feng | Dispersion shrinkage for sequencing data |
dStruct | Krishna Choudhary | Identifying differentially reactive regions from RNA structurome profiling data |
DTA | Bjoern Schwalb | Dynamic Transcriptome Analysis |
Dune | Hector Roux de Bezieux | Improving replicability in single-cell RNA-Seq cell type discovery |
dupRadar | Sergi Sayols, Holger Klein | Assessment of duplication rates in RNA-Seq datasets |
dyebias | Philip Lijnzaad | The GASSCO method for correcting for slide-dependent gene-specific dye bias |
DynDoc | Bioconductor Package Maintainer | Dynamic document tools |
easier | Oscar Lapuente-Santana | Estimate Systems Immune Response from RNA-seq data |
EasyCellType | Ruoxing Li | Annotate cell types for scRNA-seq data |
easylift | Abdullah Al Nahid | An R package to perform genomic liftover |
easyreporting | Dario Righelli | Helps creating report for improving Reproducible Computational Research |
easyRNASeq | Nicolas Delhomme | Count summarization and normalization for RNA-Seq data |
EBarrays | Ming Yuan | Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification |
EBcoexpress | John A. Dawson | EBcoexpress for Differential Co-Expression Analysis |
EBImage | Andrzej Oleś | Image processing and analysis toolbox for R |
EBSEA | Arfa Mehmood | Exon Based Strategy for Expression Analysis of genes |
EBSeq | Xiuyu Ma | An R package for gene and isoform differential expression analysis of RNA-seq data |
ecolitk | Laurent Gautier | Meta-data and tools for E. coli |
EDASeq | Davide Risso | Exploratory Data Analysis and Normalization for RNA-Seq |
edge | John D. Storey, Andrew J. Bass | Extraction of Differential Gene Expression |
edgeR | Yunshun Chen, Gordon Smyth, Aaron Lun, Mark Robinson | Empirical Analysis of Digital Gene Expression Data in R |
EDIRquery | Laura D.T. Vo Ngoc | Query the EDIR Database For Specific Gene |
eds | Avi Srivastava | eds: Low-level reader for Alevin EDS format |
EGAD | Sara Ballouz | Extending guilt by association by degree |
EGSEA | Monther Alhamdoosh | Ensemble of Gene Set Enrichment Analyses |
eiR | Thomas Girke | Accelerated similarity searching of small molecules |
eisaR | Michael Stadler | Exon-Intron Split Analysis (EISA) in R |
ELMER | Tiago Chedraoui Silva | Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes |
EMDomics | Sadhika Malladi and Daniel Schmolze | Earth Mover's Distance for Differential Analysis of Genomics Data |
EmpiricalBrownsMethod | David Gibbs | Uses Brown's method to combine p-values from dependent tests |
EnhancedVolcano | Kevin Blighe | Publication-ready volcano plots with enhanced colouring and labeling |
enhancerHomologSearch | Jianhong Ou | Identification of putative mammalian orthologs to given enhancer |
EnMCB | Xin Yu | Predicting Disease Progression Based on Methylation Correlated Blocks using Ensemble Models |
ENmix | Zongli Xu | Quality control and analysis tools for Illumina DNA methylation BeadChip |
EnrichDO | Hongyu Fu | a Global Weighted Model for Disease Ontology Enrichment Analysis |
EnrichedHeatmap | Zuguang Gu | Making Enriched Heatmaps |
EnrichmentBrowser | Ludwig Geistlinger | Seamless navigation through combined results of set-based and network-based enrichment analysis |
enrichplot | Guangchuang Yu | Visualization of Functional Enrichment Result |
enrichViewNet | Astrid Deschênes | From functional enrichment results to biological networks |
ensembldb | Johannes Rainer | Utilities to create and use Ensembl-based annotation databases |
epialleleR | Oleksii Nikolaienko | Fast, Epiallele-Aware Methylation Caller and Reporter |
EpiCompare | Thomas Roberts | Comparison, Benchmarking & QC of Epigenomic Datasets |
epidecodeR | Kandarp Joshi | epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation |
EpiDISH | Shijie C. Zheng | Epigenetic Dissection of Intra-Sample-Heterogeneity |
epigenomix | Hans-Ulrich Klein | Epigenetic and gene transcription data normalization and integration with mixture models |
epigraHMM | Pedro Baldoni | Epigenomic R-based analysis with hidden Markov models |
EpiMix | Yuanning Zheng | EpiMix: an integrative tool for the population-level analysis of DNA methylation |
epimutacions | Dolors Pelegri-Siso | Robust outlier identification for DNA methylation data |
epiNEM | Martin Pirkl | epiNEM |
epiregulon | Xiaosai Yao | Gene regulatory network inference from single cell epigenomic data |
epiregulon.extra | Xiaosai Yao | Companion package to epiregulon with additional plotting, differential and graph functions |
epistack | DEVAILLY Guillaume | Heatmaps of Stack Profiles from Epigenetic Signals |
epistasisGA | Michael Nodzenski | An R package to identify multi-snp effects in nuclear family studies using the GADGETS method |
EpiTxDb | Felix G.M. Ernst | Storing and accessing epitranscriptomic information using the AnnotationDbi interface |
epivizr | Hector Corrada Bravo | R Interface to epiviz web app |
epivizrChart | Hector Corrada Bravo | R interface to epiviz web components |
epivizrData | Hector Corrada Bravo | Data Management API for epiviz interactive visualization app |
epivizrServer | Hector Corrada Bravo | WebSocket server infrastructure for epivizr apps and packages |
epivizrStandalone | Hector Corrada Bravo | Run Epiviz Interactive Genomic Data Visualization App within R |
erccdashboard | Sarah Munro | Assess Differential Gene Expression Experiments with ERCC Controls |
erma | VJ Carey | epigenomic road map adventures |
ERSSA | Zixuan Shao | Empirical RNA-seq Sample Size Analysis |
esATAC | Zheng Wei | An Easy-to-use Systematic pipeline for ATACseq data analysis |
escape | Nick Borcherding | Easy single cell analysis platform for enrichment |
escheR | Boyi Guo | Unified multi-dimensional visualizations with Gestalt principles |
esetVis | Laure Cougnaud | Visualizations of expressionSet Bioconductor object |
eudysbiome | Xiaoyuan Zhou | Cartesian plot and contingency test on 16S Microbial data |
evaluomeR | José Antonio Bernabé-Díaz | Evaluation of Bioinformatics Metrics |
EventPointer | Juan A. Ferrer-Bonsoms | An effective identification of alternative splicing events using junction arrays and RNA-Seq data |
EWCE | Alan Murphy | Expression Weighted Celltype Enrichment |
ExCluster | R. Matthew Tanner | ExCluster robustly detects differentially expressed exons between two conditions of RNA-seq data, requiring at least two independent biological replicates per condition |
ExiMiR | Sylvain Gubian | R functions for the normalization of Exiqon miRNA array data |
ExperimentHub | Bioconductor Package Maintainer | Client to access ExperimentHub resources |
ExperimentHubData | Bioconductor Package Maintainer | Add resources to ExperimentHub |
ExperimentSubset | Irzam Sarfraz | Manages subsets of data with Bioconductor Experiment objects |
ExploreModelMatrix | Charlotte Soneson | Graphical Exploration of Design Matrices |
ExpressionAtlas | Pedro Madrigal | Download datasets from EMBL-EBI Expression Atlas |
extraChIPs | Stevie Pederson | Additional functions for working with ChIP-Seq data |
fabia | Andreas Mitterecker | FABIA: Factor Analysis for Bicluster Acquisition |
factDesign | Denise Scholtens | Factorial designed microarray experiment analysis |
factR | Fursham Hamid | Functional Annotation of Custom Transcriptomes |
faers | Yun Peng | R interface for FDA Adverse Event Reporting System |
FamAgg | Johannes Rainer | Pedigree Analysis and Familial Aggregation |
famat | Mathieu Charles | Functional analysis of metabolic and transcriptomic data |
fastLiquidAssociation | Tina Gunderson | functions for genome-wide application of Liquid Association |
FastqCleaner | Leandro Roser | A Shiny Application for Quality Control, Filtering and Trimming of FASTQ Files |
fastreeR | Anestis Gkanogiannis | Phylogenetic, Distance and Other Calculations on VCF and Fasta Files |
fastseg | Alexander Blume | fastseg - a fast segmentation algorithm |
fCCAC | Pedro Madrigal | functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets |
fCI | Shaojun Tang | f-divergence Cutoff Index for Differential Expression Analysis in Transcriptomics and Proteomics |
fcScan | Pierre Khoueiry Abdullah El-Kurdi | fcScan for detecting clusters of coordinates with user defined options |
fdrame | Effi Kenigsberg | FDR adjustments of Microarray Experiments (FDR-AME) |
FEAST | Kenong Su | FEAture SelcTion (FEAST) for Single-cell clustering |
FeatSeekR | Tuemay Capraz | FeatSeekR an R package for unsupervised feature selection |
fedup | Catherine Ross | Fisher's Test for Enrichment and Depletion of User-Defined Pathways |
FELLA | Sergio Picart-Armada | Interpretation and enrichment for metabolomics data |
fenr | Marek Gierlinski | Fast functional enrichment for interactive applications |
ffpe | Levi Waldron | Quality assessment and control for FFPE microarray expression data |
fgga | Flavio Spetale | Hierarchical ensemble method based on factor graph |
FGNet | Sara Aibar | Functional Gene Networks derived from biological enrichment analyses |
fgsea | Alexey Sergushichev | Fast Gene Set Enrichment Analysis |
FilterFFPE | Lanying Wei | FFPE Artificial Chimeric Read Filter for NGS data |
findIPs | Shuo Wang | Influential Points Detection for Feature Rankings |
FindIT2 | Guandong Shang | find influential TF and Target based on multi-omics data |
FISHalyseR | Karesh Arunakirinathan, Andreas Heindl | FISHalyseR a package for automated FISH quantification |
fishpond | Michael Love | Fishpond: downstream methods and tools for expression data |
FitHiC | Ruyu Tan | Confidence estimation for intra-chromosomal contact maps |
flagme | Mark Robinson, Riccardo Romoli | Analysis of Metabolomics GC/MS Data |
FLAMES | Changqing Wang | FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data |
flowAI | Gianni Monaco | Automatic and interactive quality control for flow cytometry data |
flowBeads | Nikolas Pontikos | flowBeads: Analysis of flow bead data |
flowBin | Kieran O'Neill | Combining multitube flow cytometry data by binning |
flowcatchR | Federico Marini | Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells |
flowCHIC | Author: Joachim Schumann | Analyze flow cytometric data using histogram information |
flowClean | Kipper Fletez-Brant | flowClean |
flowClust | Greg Finak, Mike Jiang | Clustering for Flow Cytometry |
flowCore | Mike Jiang | flowCore: Basic structures for flow cytometry data |
flowCut | Justin Meskas | Automated Removal of Outlier Events and Flagging of Files Based on Time Versus Fluorescence Analysis |
flowCyBar | Joachim Schumann | Analyze flow cytometric data using gate information |
flowDensity | Mehrnoush Malek | Sequential Flow Cytometry Data Gating |
flowFP | Herb Holyst, Wade Rogers | Fingerprinting for Flow Cytometry |
flowGate | Andrew Wight | Interactive Cytometry Gating in R |
flowGraph | Alice Yue | Identifying differential cell populations in flow cytometry data accounting for marker frequency |
flowMatch | Ariful Azad | Matching and meta-clustering in flow cytometry |
flowMeans | Nima Aghaeepour | Non-parametric Flow Cytometry Data Gating |
flowMerge | Greg Finak | Cluster Merging for Flow Cytometry Data |
flowPeaks | Yongchao Ge | An R package for flow data clustering |
flowPloidy | Tyler Smith | Analyze flow cytometer data to determine sample ploidy |
flowPlots | N. Hawkins | flowPlots: analysis plots and data class for gated flow cytometry data |
FlowSOM | Sofie Van Gassen | Using self-organizing maps for visualization and interpretation of cytometry data |
flowSpecs | Jakob Theorell | Tools for processing of high-dimensional cytometry data |
flowStats | Greg Finak, Mike Jiang | Statistical methods for the analysis of flow cytometry data |
flowTime | R. Clay Wright | Annotation and analysis of biological dynamical systems using flow cytometry |
flowTrans | Greg Finak | Parameter Optimization for Flow Cytometry Data Transformation |
flowViz | Mike Jiang | Visualization for flow cytometry |
flowVS | Ariful Azad | Variance stabilization in flow cytometry (and microarrays) |
flowWorkspace | Greg Finak, Mike Jiang | Infrastructure for representing and interacting with gated and ungated cytometry data sets. |
fmcsR | Thomas Girke | Mismatch Tolerant Maximum Common Substructure Searching |
fmrs | Farhad Shokoohi | Variable Selection in Finite Mixture of AFT Regression and FMR Models |
fobitools | Pol Castellano-Escuder | Tools for Manipulating the FOBI Ontology |
FRASER | Christian Mertes | Find RAre Splicing Events in RNA-Seq Data |
frenchFISH | Adam Berman | Poisson Models for Quantifying DNA Copy-number from FISH Images of Tissue Sections |
FRGEpistasis | Futao Zhang | Epistasis Analysis for Quantitative Traits by Functional Regression Model |
frma | Matthew N. McCall | Frozen RMA and Barcode |
frmaTools | Matthew N. McCall | Frozen RMA Tools |
funOmics | Elisa Gomez de Lope | Aggregating Omics Data into Higher-Level Functional Representations |
funtooNorm | Kathleen Klein | Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit |
FuseSOM | Elijah Willie | A Correlation Based Multiview Self Organizing Maps Clustering For IMC Datasets |
GA4GHclient | Welliton Souza | A Bioconductor package for accessing GA4GH API data servers |
GA4GHshiny | Welliton Souza | Shiny application for interacting with GA4GH-based data servers |
gaga | David Rossell | GaGa hierarchical model for high-throughput data analysis |
gage | Weijun Luo | Generally Applicable Gene-set Enrichment for Pathway Analysis |
GAprediction | Jon Bohlin | Prediction of gestational age with Illumina HumanMethylation450 data |
garfield | Valentina Iotchkova | GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction |
GARS | Mattia Chiesa | GARS: Genetic Algorithm for the identification of Robust Subsets of variables in high-dimensional and challenging datasets |
GateFinder | Nima Aghaeepour | Projection-based Gating Strategy Optimization for Flow and Mass Cytometry |
gatom | Alexey Sergushichev | Finding an Active Metabolic Module in Atom Transition Network |
GBScleanR | Tomoyuki Furuta | Error correction tool for noisy genotyping by sequencing (GBS) data |
gcapc | Mingxiang Teng | GC Aware Peak Caller |
gcatest | Alejandro Ochoa | Genotype Conditional Association TEST |
gCrisprTools | Russell Bainer | Suite of Functions for Pooled Crispr Screen QC and Analysis |
gcrma | Z. Wu | Background Adjustment Using Sequence Information |
GDCRNATools | Ruidong Li, Han Qu | GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC |
gDNAx | Robert Castelo | Diagnostics for assessing genomic DNA contamination in RNA-seq data |
gDR | Arkadiusz Gladki | Umbrella package for R packages in the gDR suite |
gDRcore | Arkadiusz Gladki | Processing functions and interface to process and analyze drug dose-response data |
gDRimport | Arkadiusz Gladki | Package for handling the import of dose-response data |
gDRstyle | Arkadiusz Gladki | A package with style requirements for the gDR suite |
gDRutils | Arkadiusz Gladki | A package with helper functions for processing drug response data |
GDSArray | Qian Liu | Representing GDS files as array-like objects |
gdsfmt | Xiuwen Zheng | R Interface to CoreArray Genomic Data Structure (GDS) Files |
GeDi | Annekathrin Nedwed | Defining and visualizing the distances between different genesets |
GEM | Hong Pan | GEM: fast association study for the interplay of Gene, Environment and Methylation |
gemini | Sidharth Jain | GEMINI: Variational inference approach to infer genetic interactions from pairwise CRISPR screens |
gemma.R | Ogan Mancarci | A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses |
genArise | IFC Development Team | Microarray Analysis tool |
geneAttribution | Arthur Wuster | Identification of candidate genes associated with genetic variation |
GeneBreak | Evert van den Broek | Gene Break Detection |
geneClassifiers | R Kuiper | Application of gene classifiers |
GeneExpressionSignature | Yang Cao | Gene Expression Signature based Similarity Metric |
genefilter | Bioconductor Package Maintainer | genefilter: methods for filtering genes from high-throughput experiments |
genefu | Benjamin Haibe-Kains | Computation of Gene Expression-Based Signatures in Breast Cancer |
GeneGA | Zhenpeng Li | Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm |
GeneGeneInteR | Mathieu Emily | Tools for Testing Gene-Gene Interaction at the Gene Level |
GeneMeta | Bioconductor Package Maintainer | MetaAnalysis for High Throughput Experiments |
GeneNetworkBuilder | Jianhong Ou | GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-seq data and Gene Expression Data |
GeneOverlap | Antnio Miguel de Jesus Domingues, Max-Planck Institute for Cell Biology and Genetics | Test and visualize gene overlaps |
geneplast | Mauro Castro | Evolutionary and plasticity analysis of orthologous groups |
geneplotter | Bioconductor Package Maintainer | Graphics related functions for Bioconductor |
geneRecommender | Greg Hather | A gene recommender algorithm to identify genes coexpressed with a query set of genes |
GeneRegionScan | Lasse Folkersen | GeneRegionScan |
geneRxCluster | Charles Berry | gRx Differential Clustering |
GeneSelectMMD | Weiliang Qiu | Gene selection based on the marginal distributions of gene profiles that characterized by a mixture of three-component multivariate distributions |
GENESIS | Stephanie M. Gogarten | GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness |
GeneStructureTools | Beth Signal | Tools for spliced gene structure manipulation and analysis |
geNetClassifier | Sara Aibar | Classify diseases and build associated gene networks using gene expression profiles |
GeneticsPed | David Henderson | Pedigree and genetic relationship functions |
GeneTonic | Federico Marini | Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis |
geneXtendeR | Bohdan Khomtchouk | Optimized Functional Annotation Of ChIP-seq Data |
GENIE3 | Van Anh Huynh-Thu | GEne Network Inference with Ensemble of trees |
genoCN | Wei Sun | genotyping and copy number study tools |
genomation | Altuna Akalin, Vedran Franke, Katarzyna Wreczycka | Summary, annotation and visualization of genomic data |
GenomAutomorphism | Robersy Sanchez | Compute the automorphisms between DNA's Abelian group representations |
GenomeInfoDb | Hervé Pagès | Utilities for manipulating chromosome names, including modifying them to follow a particular naming style |
genomeIntervals | Julien Gagneur | Operations on genomic intervals |
genomes | Chris Stubben | Genome sequencing project metadata |
GenomicAlignments | Hervé Pagès | Representation and manipulation of short genomic alignments |
GenomicDataCommons | Sean Davis | NIH / NCI Genomic Data Commons Access |
GenomicDistributions | Kristyna Kupkova | GenomicDistributions: fast analysis of genomic intervals with Bioconductor |
GenomicFeatures | H. Pagès | Conveniently import and query gene models |
GenomicFiles | Bioconductor Package Maintainer | Distributed computing by file or by range |
genomicInstability | Mariano Alvarez | Genomic Instability estimation for scRNA-Seq |
GenomicInteractionNodes | Jianhong Ou | A R/Bioconductor package to detect the interaction nodes from HiC/HiChIP/HiCAR data |
GenomicInteractions | Liz Ing-Simmons | Utilities for handling genomic interaction data |
GenomicOZone | Hua Zhong, Mingzhou Song | Delineate outstanding genomic zones of differential gene activity |
GenomicPlot | Shuye Pu | Plot profiles of next generation sequencing data in genomic features |
GenomicRanges | Hervé Pagès | Representation and manipulation of genomic intervals |
GenomicScores | Robert Castelo | Infrastructure to work with genomewide position-specific scores |
GenomicSuperSignature | Sehyun Oh | Interpretation of RNA-seq experiments through robust, efficient comparison to public databases |
GenomicTuples | Peter Hickey | Representation and Manipulation of Genomic Tuples |
GenProSeq | Dongmin Jung | Generating Protein Sequences with Deep Generative Models |
GenVisR | Zachary Skidmore | Genomic Visualizations in R |
GeoDiff | Nicole Ortogero | Count model based differential expression and normalization on GeoMx RNA data |
GEOexplorer | Guy Hunt | GEOexplorer: a webserver for gene expression analysis and visualisation |
GEOfastq | Alex Pickering | Downloads ENA Fastqs With GEO Accessions |
GEOmetadb | Jack Zhu | A compilation of metadata from NCBI GEO |
GeomxTools | Maddy Griswold | NanoString GeoMx Tools |
GEOquery | Sean Davis | Get data from NCBI Gene Expression Omnibus (GEO) |
GEOsubmission | Alexandre Kuhn | Prepares microarray data for submission to GEO |
GeoTcgaData | Erqiang Hu | Processing Various Types of Data on GEO and TCGA |
gep2pep | Francesco Napolitano | Creation and Analysis of Pathway Expression Profiles (PEPs) |
gespeR | Fabian Schmich | Gene-Specific Phenotype EstimatoR |
getDEE2 | Mark Ziemann | Programmatic access to the DEE2 RNA expression dataset |
geva | Itamar José Guimarães Nunes | Gene Expression Variation Analysis (GEVA) |
GEWIST | Wei Q. Deng | Gene Environment Wide Interaction Search Threshold |
gg4way | Benjamin I Laufer | 4way Plots of Differential Expression |
ggbio | Michael Lawrence | Visualization tools for genomic data |
ggcyto | Mike Jiang | Visualize Cytometry data with ggplot |
ggkegg | Noriaki Sato | Analyzing and visualizing KEGG information using the grammar of graphics |
ggmanh | John Lee | Visualization Tool for GWAS Result |
ggmsa | Lang Zhou | Plot Multiple Sequence Alignment using 'ggplot2' |
GGPA | Dongjun Chung | graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture |
ggsc | Guangchuang Yu | Visualizing Single Cell and Spatial Transcriptomics |
ggseqalign | Simeon Lim Rossmann | Minimal Visualization of Sequence Alignments |
ggspavis | Lukas M. Weber | Visualization functions for spatial transcriptomics data |
ggtree | Guangchuang Yu | an R package for visualization of tree and annotation data |
ggtreeDendro | Guangchuang Yu | Drawing 'dendrogram' using 'ggtree' |
ggtreeExtra | Shuangbin Xu | An R Package To Add Geometric Layers On Circular Or Other Layout Tree Of "ggtree" |
ggtreeSpace | Guangchuang Yu | Visualizing Phylomorphospaces using 'ggtree' |
GIGSEA | Shijia Zhu | Genotype Imputed Gene Set Enrichment Analysis |
ginmappeR | Fernando Sola | Gene Identifier Mapper |
gINTomics | Angelo Velle | Multi-Omics data integration |
girafe | J. Toedling | Genome Intervals and Read Alignments for Functional Exploration |
GLAD | Philippe Hupe | Gain and Loss Analysis of DNA |
GladiaTOX | PMP S.A. R Support | R Package for Processing High Content Screening data |
Glimma | Shian Su | Interactive visualizations for gene expression analysis |
glmGamPoi | Constantin Ahlmann-Eltze | Fit a Gamma-Poisson Generalized Linear Model |
glmSparseNet | André Veríssimo | Network Centrality Metrics for Elastic-Net Regularized Models |
GlobalAncova | Manuela Hummel | Global test for groups of variables via model comparisons |
globalSeq | Armin Rauschenberger | Global Test for Counts |
globaltest | Jelle Goeman | Testing Groups of Covariates/Features for Association with a Response Variable, with Applications to Gene Set Testing |
GloScope | William Torous | Population-level Representation on scRNA-Seq data |
gmapR | Michael Lawrence | An R interface to the GMAP/GSNAP/GSTRUCT suite |
GmicR | Richard Virgen-Slane | Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC) |
gmoviz | Kathleen Zeglinski | Seamless visualization of complex genomic variations in GMOs and edited cell lines |
GMRP | Yuan-De Tan | GWAS-based Mendelian Randomization and Path Analyses |
GNET2 | Chen Chen | Constructing gene regulatory networks from expression data through functional module inference |
GNOSIS | Lydia King | Genomics explorer using statistical and survival analysis in R |
GOexpress | Kevin Rue-Albrecht | Visualise microarray and RNAseq data using gene ontology annotations |
GOfuncR | Steffi Grote | Gene ontology enrichment using FUNC |
GOpro | Lidia Chrabaszcz | Find the most characteristic gene ontology terms for groups of human genes |
goProfiles | Alex Sanchez | goProfiles: an R package for the statistical analysis of functional profiles |
GOSemSim | Guangchuang Yu | GO-terms Semantic Similarity Measures |
goseq | Federico Marini | Gene Ontology analyser for RNA-seq and other length biased data |
goSorensen | Pablo Flores | Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO) |
goSTAG | Brian D. Bennett | A tool to use GO Subtrees to Tag and Annotate Genes within a set |
GOstats | Bioconductor Package Maintainer | Tools for manipulating GO and microarrays |
GOTHiC | Borbala Mifsud | Binomial test for Hi-C data analysis |
goTools | Agnes Paquet | Functions for Gene Ontology database |
GPA | Dongjun Chung | GPA (Genetic analysis incorporating Pleiotropy and Annotation) |
gpls | Bioconductor Package Maintainer | Classification using generalized partial least squares |
gpuMagic | Jiefei Wang | An openCL compiler with the capacity to compile R functions and run the code on GPU |
GrafGen | William Wheeler | Classification of Helicobacter Pylori Genomes |
GRaNIE | Christian Arnold | GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using single-cell or bulk chromatin accessibility and RNA-seq data |
granulator | Sabina Pfister | Rapid benchmarking of methods for *in silico* deconvolution of bulk RNA-seq data |
graper | Britta Velten | Adaptive penalization in high-dimensional regression and classification with external covariates using variational Bayes |
graph | Bioconductor Package Maintainer | graph: A package to handle graph data structures |
GraphAlignment | Joern P. Meier | GraphAlignment |
GraphAT | Thomas LaFramboise | Graph Theoretic Association Tests |
graphite | Gabriele Sales | GRAPH Interaction from pathway Topological Environment |
GraphPAC | Gregory Ryslik | Identification of Mutational Clusters in Proteins via a Graph Theoretical Approach. |
GRENITS | Edward Morrissey | Gene Regulatory Network Inference Using Time Series |
GreyListChIP | Matt Eldridge | Grey Lists -- Mask Artefact Regions Based on ChIP Inputs |
GRmetrics | Nicholas Clark, Mario Medvedovic | Calculate growth-rate inhibition (GR) metrics |
groHMM | Tulip Nandu, W. Lee Kraus | GRO-seq Analysis Pipeline |
GSALightning | Billy Heung Wing Chang | Fast Permutation-based Gene Set Analysis |
GSAR | Yasir Rahmatallah, Galina Glazko | Gene Set Analysis in R |
GSCA | Zhicheng Ji | GSCA: Gene Set Context Analysis |
gscreend | Katharina Imkeller | Analysis of pooled genetic screens |
GSEABase | Bioconductor Package Maintainer | Gene set enrichment data structures and methods |
GSEABenchmarkeR | Ludwig Geistlinger | Reproducible GSEA Benchmarking |
GSEAlm | Assaf Oron | Linear Model Toolset for Gene Set Enrichment Analysis |
GSEAmining | Oriol Arqués | Make Biological Sense of Gene Set Enrichment Analysis Outputs |
gsean | Dongmin Jung | Gene Set Enrichment Analysis with Networks |
GSgalgoR | Carlos Catania | An Evolutionary Framework for the Identification and Study of Prognostic Gene Expression Signatures in Cancer |
GSReg | Bahman Afsari, Elana J. Fertig | Gene Set Regulation (GS-Reg) |
GSRI | Julian Gehring | Gene Set Regulation Index |
GSVA | Robert Castelo | Gene Set Variation Analysis for Microarray and RNA-Seq Data |
gtrellis | Zuguang Gu | Genome Level Trellis Layout |
GUIDEseq | Lihua Julie Zhu | GUIDE-seq and PEtag-seq analysis pipeline |
Guitar | Jia Meng | Guitar |
Gviz | Robert Ivanek | Plotting data and annotation information along genomic coordinates |
GWAS.BAYES | Jacob Williams | Bayesian analysis of Gaussian GWAS data |
gwascat | VJ Carey | representing and modeling data in the EMBL-EBI GWAS catalog |
GWASTools | Stephanie M. Gogarten | Tools for Genome Wide Association Studies |
gwasurvivr | Abbas Rizvi | gwasurvivr: an R package for genome wide survival analysis |
GWENA | Gwenaëlle Lemoine | Pipeline for augmented co-expression analysis |
gypsum | Aaron Lun | Interface to the gypsum REST API |
h5vc | Paul Theodor Pyl | Managing alignment tallies using a hdf5 backend |
hapFabia | Andreas Mitterecker | hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data |
Harman | Jason Ross | The removal of batch effects from datasets using a PCA and constrained optimisation based technique |
HarmonizR | Simon Schlumbohm | Handles missing values and makes more data available |
Harshlight | Maurizio Pellegrino | A "corrective make-up" program for microarray chips |
hca | Martin Morgan | Exploring the Human Cell Atlas Data Coordinating Platform |
HDF5Array | Hervé Pagès | HDF5 backend for DelayedArray objects |
HDTD | Anestis Touloumis | Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD) |
hdxmsqc | Oliver M. Crook | An R package for quality Control for hydrogen deuterium exchange mass spectrometry experiments |
heatmaps | Malcolm Perry | Flexible Heatmaps for Functional Genomics and Sequence Features |
Heatplus | Alexander Ploner | Heatmaps with row and/or column covariates and colored clusters |
HelloRanges | Michael Lawrence | Introduce *Ranges to bedtools users |
HELP | Reid F. Thompson | Tools for HELP data analysis |
HEM | HyungJun Cho | Heterogeneous error model for identification of differentially expressed genes under multiple conditions |
hermes | Daniel Sabanés Bové | Preprocessing, analyzing, and reporting of RNA-seq data |
HERON | Sean McIlwain | Hierarchical Epitope pROtein biNding |
Herper | Thomas Carroll | The Herper package is a simple toolset to install and manage conda packages and environments from R |
HGC | XGlab | A fast hierarchical graph-based clustering method |
hiAnnotator | Nirav V Malani | Functions for annotating GRanges objects |
HIBAG | Xiuwen Zheng | HLA Genotype Imputation with Attribute Bagging |
HicAggR | Olivier Cuvier | Set of 3D genomic interaction analysis tools |
HiCBricks | Koustav Pal | Framework for Storing and Accessing Hi-C Data Through HDF Files |
HiCcompare | Mikhail Dozmorov | HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets |
HiCDCPlus | Merve Sahin | Hi-C Direct Caller Plus |
HiCDOC | Maigné Élise | A/B compartment detection and differential analysis |
HiCExperiment | Jacques Serizay | Bioconductor class for interacting with Hi-C files in R |
HiContacts | Jacques Serizay | Analysing cool files in R with HiContacts |
HiCool | Jacques Serizay | HiCool |
hicVennDiagram | Jianhong Ou | Venn Diagram for genomic interaction data |
hierGWAS | Laura Buzdugan | Asessing statistical significance in predictive GWA studies |
hierinf | Claude Renaux | Hierarchical Inference |
HilbertCurve | Zuguang Gu | Making 2D Hilbert Curve |
HilbertVis | Simon Anders | Hilbert curve visualization |
HilbertVisGUI | Simon Anders | HilbertVisGUI |
HiLDA | Zhi Yang | Conducting statistical inference on comparing the mutational exposures of mutational signatures by using hierarchical latent Dirichlet allocation |
hipathia | Marta R. Hidalgo | HiPathia: High-throughput Pathway Analysis |
HIPPO | Tae Kim | Heterogeneity-Induced Pre-Processing tOol |
hiReadsProcessor | Nirav V Malani | Functions to process LM-PCR reads from 454/Illumina data |
HIREewas | Xiangyu Luo | Detection of cell-type-specific risk-CpG sites in epigenome-wide association studies |
HiTC | Nicolas Servant | High Throughput Chromosome Conformation Capture analysis |
hmdbQuery | VJ Carey | utilities for exploration of human metabolome database |
HMMcopy | Daniel Lai | Copy number prediction with correction for GC and mappability bias for HTS data |
HoloFoodR | Tuomas Borman | R interface to EBI HoloFood resource |
hoodscanR | Ning Liu | Spatial cellular neighbourhood scanning in R |
hopach | Katherine S. Pollard | Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) |
HPAanalyze | Anh Nhat Tran | Retrieve and analyze data from the Human Protein Atlas |
hpar | Laurent Gatto | Human Protein Atlas in R |
HPiP | Matineh Rahmatbakhsh | Host-Pathogen Interaction Prediction |
HTqPCR | Heidi Dvinge | Automated analysis of high-throughput qPCR data |
HTSeqGenie | Jens Reeder | A NGS analysis pipeline. |
HTSFilter | Andrea Rau | Filter replicated high-throughput transcriptome sequencing data |
HubPub | Kayla Interdonato | Utilities to create and use Bioconductor Hubs |
hummingbird | Eleni Adam | Bayesian Hidden Markov Model for the detection of differentially methylated regions |
HybridExpress | Fabricio Almeida-Silva | Comparative analysis of RNA-seq data for hybrids and their progenitors |
HybridMTest | Demba Fofana | Hybrid Multiple Testing |
hypeR | Anthony Federico | An R Package For Geneset Enrichment Workflows |
hyperdraw | Paul Murrell | Visualizing Hypergaphs |
hypergraph | Bioconductor Package Maintainer | A package providing hypergraph data structures |
iASeq | Yingying Wei | iASeq: integrating multiple sequencing datasets for detecting allele-specific events |
iasva | Donghyung Lee, Anthony Cheng | Iteratively Adjusted Surrogate Variable Analysis |
iBBiG | Aedin Culhane | Iterative Binary Biclustering of Genesets |
ibh | Kircicegi Korkmaz | Interaction Based Homogeneity for Evaluating Gene Lists |
iBMQ | Greg Imholte | integrated Bayesian Modeling of eQTL data |
iCARE | Parichoy Pal Choudhury | Individualized Coherent Absolute Risk Estimation (iCARE) |
Icens | Bioconductor Package Maintainer | NPMLE for Censored and Truncated Data |
icetea | Vivek Bhardwaj | Integrating Cap Enrichment with Transcript Expression Analysis |
iCheck | Weiliang Qiu | QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data |
iChip | Qianxing Mo | Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models |
iClusterPlus | Qianxing Mo, Ronglai Shen | Integrative clustering of multi-type genomic data |
iCNV | Zilu Zhou | Integrated Copy Number Variation detection |
iCOBRA | Charlotte Soneson | Comparison and Visualization of Ranking and Assignment Methods |
ideal | Federico Marini | Interactive Differential Expression AnaLysis |
IdeoViz | Shraddha Pai | Plots data (continuous/discrete) along chromosomal ideogram |
idiogram | Karl J. Dykema | idiogram |
idpr | William M. McFadden | Profiling and Analyzing Intrinsically Disordered Proteins in R |
idr2d | Konstantin Krismer | Irreproducible Discovery Rate for Genomic Interactions Data |
IFAA | Zhigang Li | Robust Inference for Absolute Abundance in Microbiome Analysis |
iGC | Liang-Bo Wang | An integrated analysis package of Gene expression and Copy number alteration |
IgGeneUsage | Simo Kitanovski | Differential gene usage in immune repertoires |
igvR | Arkadiusz Gladki | igvR: integrative genomics viewer |
igvShiny | Arkadiusz Gladki | igvShiny: a wrapper of Integrative Genomics Viewer (IGV - an interactive tool for visualization and exploration integrated genomic data) |
IHW | Nikos Ignatiadis | Independent Hypothesis Weighting |
illuminaio | Kasper Daniel Hansen | Parsing Illumina Microarray Output Files |
ILoReg | Johannes Smolander | ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data |
IMAS | Seonggyun Han | Integrative analysis of Multi-omics data for Alternative Splicing |
imcRtools | Daniel Schulz | Methods for imaging mass cytometry data analysis |
IMMAN | Minoo Ashtiani | Interlog protein network reconstruction by Mapping and Mining ANalysis |
immunoClust | Till Soerensen | immunoClust - Automated Pipeline for Population Detection in Flow Cytometry |
immunogenViewer | Katharina Waury | Visualization and evaluation of protein immunogens |
immunotation | Katharina Imkeller | Tools for working with diverse immune genes |
IMPCdata | Jeremy Mason | Retrieves data from IMPC database |
impute | Balasubramanian Narasimhan | impute: Imputation for microarray data |
INDEED | Ressom group, Yiming Zuo | Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package |
iNETgrate | Habil Zare | Integrates DNA methylation data with gene expression in a single gene network |
infercnv | Christophe Georgescu | Infer Copy Number Variation from Single-Cell RNA-Seq Data |
infinityFlow | Etienne Becht | Augmenting Massively Parallel Cytometry Experiments Using Multivariate Non-Linear Regressions |
Informeasure | Chu Pan | R implementation of information measures |
InPAS | Jianhong Ou | Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data |
INPower | Bill Wheeler | An R package for computing the number of susceptibility SNPs |
INSPEcT | Stefano de Pretis, Mattia Furlan | Modeling RNA synthesis, processing and degradation with RNA-seq data |
INTACT | Jeffrey Okamoto | Integrate TWAS and Colocalization Analysis for Gene Set Enrichment Analysis |
InTAD | Konstantin Okonechnikov | Search for correlation between epigenetic signals and gene expression in TADs |
intansv | Wen Yao | Integrative analysis of structural variations |
interacCircos | Zhe Cui | The Generation of Interactive Circos Plot |
InteractionSet | Aaron Lun | Base Classes for Storing Genomic Interaction Data |
InteractiveComplexHeatmap | Zuguang Gu | Make Interactive Complex Heatmaps |
interactiveDisplay | Bioconductor Package Maintainer | Package for enabling powerful shiny web displays of Bioconductor objects |
interactiveDisplayBase | Bioconductor Package Maintainer | Base package for enabling powerful shiny web displays of Bioconductor objects |
InterCellar | Marta Interlandi | InterCellar: an R-Shiny app for interactive analysis and exploration of cell-cell communication in single-cell transcriptomics |
IntEREst | Ali Oghabian | Intron-Exon Retention Estimator |
IntramiRExploreR | Surajit Bhattacharya | Predicting Targets for Drosophila Intragenic miRNAs |
IONiseR | Mike Smith | Quality Assessment Tools for Oxford Nanopore MinION data |
iPAC | Gregory Ryslik | Identification of Protein Amino acid Clustering |
iPath | Kenong Su | iPath pipeline for detecting perturbed pathways at individual level |
ipdDb | Steffen Klasberg | IPD IMGT/HLA and IPD KIR database for Homo sapiens |
IPO | Thomas Lieb | Automated Optimization of XCMS Data Processing parameters |
IRanges | Hervé Pagès | Foundation of integer range manipulation in Bioconductor |
ISAnalytics | Giulia Pais | Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies |
iSEE | Kevin Rue-Albrecht | Interactive SummarizedExperiment Explorer |
iSEEde | Kevin Rue-Albrecht | iSEE extension for panels related to differential expression analysis |
iSEEfier | Najla Abassi | Streamlining the creation of initial states for starting an iSEE instance |
iSEEhex | Kevin Rue-Albrecht | iSEE extension for summarising data points in hexagonal bins |
iSEEhub | Kevin Rue-Albrecht | iSEE for the Bioconductor ExperimentHub |
iSEEindex | Kevin Rue-Albrecht | iSEE extension for a landing page to a custom collection of data sets |
iSEEpathways | Kevin Rue-Albrecht | iSEE extension for panels related to pathway analysis |
iSEEtree | Giulio Benedetti | Interactive visualisation for microbiome data |
iSEEu | Kevin Rue-Albrecht | iSEE Universe |
iSeq | Qianxing Mo | Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising Models |
ISLET | Hao Feng | Individual-Specific ceLl typE referencing Tool |
isobar | Florian P Breitwieser | Analysis and quantitation of isobarically tagged MSMS proteomics data |
IsoBayes | Simone Tiberi | IsoBayes: Single Isoform protein inference Method via Bayesian Analyses |
IsoCorrectoR | Christian Kohler | Correction for natural isotope abundance and tracer purity in MS and MS/MS data from stable isotope labeling experiments |
IsoCorrectoRGUI | Christian Kohler | Graphical User Interface for IsoCorrectoR |
IsoformSwitchAnalyzeR | Kristoffer Vitting-Seerup | Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data |
ISoLDE | Christelle Reynès | Integrative Statistics of alleLe Dependent Expression |
isomiRs | Lorena Pantano | Analyze isomiRs and miRNAs from small RNA-seq |
ITALICS | Guillem Rigaill | ITALICS |
iterativeBMA | Ka Yee Yeung | The Iterative Bayesian Model Averaging (BMA) algorithm |
iterativeBMAsurv | Ka Yee Yeung | The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis |
IVAS | Seonggyun Han | Identification of genetic Variants affecting Alternative Splicing |
ivygapSE | VJ Carey | A SummarizedExperiment for Ivy-GAP data |
IWTomics | Marzia A Cremona | Interval-Wise Testing for Omics Data |
karyoploteR | Bernat Gel | Plot customizable linear genomes displaying arbitrary data |
katdetectr | Daan Hazelaar | Detection, Characterization and Visualization of Kataegis in Sequencing Data |
KBoost | Luis F. Iglesias-Martinez | Inference of gene regulatory networks from gene expression data |
KCsmart | Jorma de Ronde | Multi sample aCGH analysis package using kernel convolution |
kebabs | Ulrich Bodenhofer | Kernel-Based Analysis of Biological Sequences |
KEGGgraph | Jitao David Zhang | KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor |
KEGGlincs | Shana White, Mario Medvedovic | Visualize all edges within a KEGG pathway and overlay LINCS data |
keggorthology | VJ Carey | graph support for KO, KEGG Orthology |
KEGGREST | Bioconductor Package Maintainer | Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG) |
KinSwingR | Ashley J. Waardenberg | KinSwingR: network-based kinase activity prediction |
kissDE | Aurélie Siberchicot | Retrieves Condition-Specific Variants in RNA-Seq Data |
kmcut | Igor Kuznetsov | Optimized Kaplan Meier analysis and identification and validation of prognostic biomarkers |
KnowSeq | Daniel Castillo-Secilla | KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline |
knowYourCG | Goldberg David | Functional analysis of DNA methylome datasets |
LACE | Davide Maspero | Longitudinal Analysis of Cancer Evolution (LACE) |
lapmix | Yann Ruffieux | Laplace Mixture Model in Microarray Experiments |
LBE | Cyril Dalmasso | Estimation of the false discovery rate. |
ldblock | VJ Carey | data structures for linkage disequilibrium measures in populations |
LEA | Olivier Francois, Eric Frichot | LEA: an R package for Landscape and Ecological Association Studies |
LedPred | Aitor Gonzalez | Learning from DNA to Predict Enhancers |
lefser | Sehyun Oh | R implementation of the LEfSE method for microbiome biomarker discovery |
lemur | Constantin Ahlmann-Eltze | Latent Embedding Multivariate Regression |
les | Julian Gehring | Identifying Differential Effects in Tiling Microarray Data |
levi | Jose Luiz Rybarczyk Filho | Landscape Expression Visualization Interface |
lfa | Alejandro Ochoa | Logistic Factor Analysis for Categorical Data |
limma | Gordon Smyth | Linear Models for Microarray and Omics Data |
limmaGUI | Gordon Smyth | GUI for limma Package With Two Color Microarrays |
limpca | Manon Martin | An R package for the linear modeling of high-dimensional designed data based on ASCA/APCA family of methods |
lineagespot | Nikolaos Pechlivanis | Detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing |
LinkHD | "Laura M Zingaretti" | LinkHD: a versatile framework to explore and integrate heterogeneous data |
Linnorm | Shun Hang Yip | Linear model and normality based normalization and transformation method (Linnorm) |
LinTInd | Luyue Wang | Lineage tracing by indels |
lionessR | Ping-Han Hsieh | Modeling networks for individual samples using LIONESS |
lipidr | Ahmed Mohamed | Data Mining and Analysis of Lipidomics Datasets |
LiquidAssociation | Yen-Yi Ho | LiquidAssociation |
lisaClust | Ellis Patrick | lisaClust: Clustering of Local Indicators of Spatial Association |
lmdme | Cristobal Fresno | Linear Model decomposition for Designed Multivariate Experiments |
LOBSTAHS | Henry Holm, Daniel Lowenstein, James Collins | Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences |
loci2path | Tianlei Xu | Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs |
logicFS | Holger Schwender | Identification of SNP Interactions |
LOLA | Nathan Sheffield | Locus overlap analysis for enrichment of genomic ranges |
LoomExperiment | Bioconductor Package Maintainer | LoomExperiment container |
LPE | Nitin Jain | Methods for analyzing microarray data using Local Pooled Error (LPE) method |
lpNet | Lars Kaderali | Linear Programming Model for Network Inference |
lpsymphony | Vladislav Kim | Symphony integer linear programming solver in R |
LRBaseDbi | Koki Tsuyuzaki | DBI to construct LRBase-related package |
LRcell | Wenjing Ma | Differential cell type change analysis using Logistic/linear Regression |
lumi | Lei Huang | BeadArray Specific Methods for Illumina Methylation and Expression Microarrays |
lute | Sean K Maden | Framework for cell size scale factor normalized bulk transcriptomics deconvolution experiments |
LymphoSeq | David Coffey | Analyze high-throughput sequencing of T and B cell receptors |
M3C | Christopher John | Monte Carlo Reference-based Consensus Clustering |
M3Drop | Tallulah Andrews | Michaelis-Menten Modelling of Dropouts in single-cell RNASeq |
m6Aboost | You Zhou | m6Aboost |
Maaslin2 | Lauren McIver | "Multivariable Association Discovery in Population-scale Meta-omics Studies" |
Macarron | Sagun Maharjan | Prioritization of potentially bioactive metabolic features from epidemiological and environmental metabolomics datasets |
maCorrPlot | Alexander Ploner | Visualize artificial correlation in microarray data |
MACSQuantifyR | Raphaël Bonnet | Fast treatment of MACSQuantify FACS data |
MACSr | Qiang Hu | MACS: Model-based Analysis for ChIP-Seq |
made4 | Aedin Culhane | Multivariate analysis of microarray data using ADE4 |
MADSEQ | Yu Kong | Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data |
maftools | Anand Mayakonda | Summarize, Analyze and Visualize MAF Files |
MAGAR | Michael Scherer | MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data |
MAGeCKFlute | Wubing Zhang | Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens |
magpie | Daoyu Duan | MeRIP-Seq data Analysis for Genomic Power Investigation and Evaluation |
magrene | Fabrício Almeida-Silva | Motif Analysis In Gene Regulatory Networks |
MAI | Jonathan Dekermanjian | Mechanism-Aware Imputation |
MAIT | Pol Sola-Santos | Statistical Analysis of Metabolomic Data |
makecdfenv | James W. MacDonald | CDF Environment Maker |
MANOR | Pierre Neuvial | CGH Micro-Array NORmalization |
MantelCorr | Brian Steinmeyer | Compute Mantel Cluster Correlations |
MAPFX | Hsiao-Chi Liao | MAssively Parallel Flow cytometry Xplorer (MAPFX): A Toolbox for Analysing Data from the Massively-Parallel Cytometry Experiments |
maPredictDSC | Adi Laurentiu Tarca | Phenotype prediction using microarray data: approach of the best overall team in the IMPROVER Diagnostic Signature Challenge |
mapscape | Maia Smith | mapscape |
mariner | Eric Davis | Mariner: Explore the Hi-Cs |
marr | Tusharkanti Ghosh | Maximum rank reproducibility |
marray | Yee Hwa (Jean) Yang | Exploratory analysis for two-color spotted microarray data |
martini | Hector Climente-Gonzalez | GWAS Incorporating Networks |
maser | Diogo F.T. Veiga | Mapping Alternative Splicing Events to pRoteins |
maSigPro | Maria Jose Nueda | Significant Gene Expression Profile Differences in Time Course Gene Expression Data |
maskBAD | Michael Dannemann | Masking probes with binding affinity differences |
MassArray | Reid F. Thompson | Analytical Tools for MassArray Data |
massiR | Sam Buckberry | massiR: MicroArray Sample Sex Identifier |
MassSpecWavelet | Sergio Oller Moreno | Peak Detection for Mass Spectrometry data using wavelet-based algorithms |
MAST | Andrew McDavid | Model-based Analysis of Single Cell Transcriptomics |
mastR | Jinjin Chen | Markers Automated Screening Tool in R |
matchBox | Luigi Marchionni, Anuj Gupta | Utilities to compute, compare, and plot the agreement between ordered vectors of features (ie. distinct genomic experiments). The package includes Correspondence-At-the-TOP (CAT) analysis. |
MatrixGenerics | Peter Hickey | S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects |
MatrixQCvis | Thomas Naake | Shiny-based interactive data-quality exploration for omics data |
MatrixRider | Elena Grassi | Obtain total affinity and occupancies for binding site matrices on a given sequence |
matter | Kylie A. Bemis | Out-of-core statistical computing and signal processing |
MBAmethyl | Tao Wang | Model-based analysis of DNA methylation data |
MBASED | Oleg Mayba | Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection |
MBCB | Bo Yao | MBCB (Model-based Background Correction for Beadarray) |
MBECS | Michael Olbrich | Evaluation and correction of batch effects in microbiome data-sets |
mbkmeans | Davide Risso | Mini-batch K-means Clustering for Single-Cell RNA-seq |
mBPCR | P.M.V. Rancoita | Bayesian Piecewise Constant Regression for DNA copy number estimation |
MBQN | Eva Brombacher | Mean/Median-balanced quantile normalization |
mbQTL | Mercedeh Movassagh | mbQTL: A package for SNP-Taxa mGWAS analysis |
MBttest | Yuan-De Tan | Multiple Beta t-Tests |
MCbiclust | Robert Bentham | Massive correlating biclusters for gene expression data and associated methods |
mCSEA | Jordi Martorell-Marugán | Methylated CpGs Set Enrichment Analysis |
mdp | Helder Nakaya | Molecular Degree of Perturbation calculates scores for transcriptome data samples based on their perturbation from controls |
mdqc | Gabriela Cohen-Freue | Mahalanobis Distance Quality Control for microarrays |
MDTS | Jack M.. Fu | Detection of de novo deletion in targeted sequencing trios |
MEAL | Xavier Escribà Montagut | Perform methylation analysis |
MeasurementError.cor | Beiying Ding | Measurement Error model estimate for correlation coefficient |
MEAT | Sarah Voisin | Muscle Epigenetic Age Test |
MEB | Jiadi Zhu, Yan Zhou | A normalization-invariant minimum enclosing ball method to detect differentially expressed genes for RNA-seq and scRNA-seq data |
MEDIPS | Lukas Chavez | DNA IP-seq data analysis |
MEDME | Mattia Pelizzola | Modelling Experimental Data from MeDIP Enrichment |
megadepth | David Zhang | megadepth: BigWig and BAM related utilities |
MEIGOR | Jose A. Egea | MEIGOR - MEtaheuristics for bIoinformatics Global Optimization |
Melissa | C. A. Kapourani | Bayesian clustering and imputationa of single cell methylomes |
memes | Spencer Nystrom | motif matching, comparison, and de novo discovery using the MEME Suite |
Mergeomics | Zeyneb Kurt | Integrative network analysis of omics data |
MeSHDbi | Koki Tsuyuzaki | DBI to construct MeSH-related package from sqlite file |
meshes | Guangchuang Yu | MeSH Enrichment and Semantic analyses |
meshr | Koki Tsuyuzaki | Tools for conducting enrichment analysis of MeSH |
MesKit | Mengni Liu | A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic alterations |
messina | Mark Pinese | Single-gene classifiers and outlier-resistant detection of differential expression for two-group and survival problems |
metabCombiner | Hani Habra | Method for Combining LC-MS Metabolomics Feature Measurements |
metabinR | Anestis Gkanogiannis | Abundance and Compositional Based Binning of Metagenomes |
MetaboAnnotation | Johannes Rainer | Utilities for Annotation of Metabolomics Data |
MetaboCoreUtils | Johannes Rainer | Core Utils for Metabolomics Data |
metabolomicsWorkbenchR | Gavin Rhys Lloyd | Metabolomics Workbench in R |
metabomxtr | Michael Nodzenski | A package to run mixture models for truncated metabolomics data with normal or lognormal distributions |
MetaboSignal | Andrea Rodriguez-Martinez, Rafael Ayala | MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways |
metaCCA | Anna Cichonska | Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide Association Studies Using Canonical Correlation Analysis |
MetaCyto | Zicheng Hu | MetaCyto: A package for meta-analysis of cytometry data |
metagene2 | Eric Fournier | A package to produce metagene plots |
metagenomeSeq | Joseph N. Paulson | Statistical analysis for sparse high-throughput sequencing |
metahdep | John R. Stevens | Hierarchical Dependence in Meta-Analysis |
metaMS | Yann Guitton | MS-based metabolomics annotation pipeline |
MetaNeighbor | Stephan Fischer | Single cell replicability analysis |
MetaPhOR | Emily Isenhart | Metabolic Pathway Analysis of RNA |
metapod | Aaron Lun | Meta-Analyses on P-Values of Differential Analyses |
metapone | Tianwei Yu | Conducts pathway test of metabolomics data using a weighted permutation test |
metaSeq | Koki Tsuyuzaki | Meta-analysis of RNA-Seq count data in multiple studies |
metaseqR2 | Panagiotis Moulos | An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms |
MetCirc | Thomas Naake | Navigating mass spectral similarity in high-resolution MS/MS metabolomics data metabolomics data |
methimpute | Aaron Taudt | Imputation-guided re-construction of complete methylomes from WGBS data |
methInheritSim | Pascal Belleau | Simulating Whole-Genome Inherited Bisulphite Sequencing Data |
methodical | Richard Heery | Discovering genomic regions where methylation is strongly associated with transcriptional activity |
MethPed | Helena Carén | A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes |
MethReg | Tiago Silva | Assessing the regulatory potential of DNA methylation regions or sites on gene transcription |
methrix | Anand Mayakonda | Fast and efficient summarization of generic bedGraph files from Bisufite sequencing |
MethTargetedNGS | Muhammad Ahmer Jamil | Perform Methylation Analysis on Next Generation Sequencing Data |
MethylAid | L.J.Sinke | Visual and interactive quality control of large Illumina DNA Methylation array data sets |
methylCC | Stephanie C. Hicks | Estimate the cell composition of whole blood in DNA methylation samples |
methylclock | Dolors Pelegri-Siso | Methylclock - DNA methylation-based clocks |
methylGSA | Xu Ren | Gene Set Analysis Using the Outcome of Differential Methylation |
methyLImp2 | Anna Plaksienko | Missing value estimation of DNA methylation data |
methylInheritance | Astrid Deschênes | Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect |
methylKit | Altuna Akalin, Alexander Blume | DNA methylation analysis from high-throughput bisulfite sequencing results |
MethylMix | Olivier Gevaert | MethylMix: Identifying methylation driven cancer genes |
methylMnM | Yan Zhou | detect different methylation level (DMR) |
methylPipe | Mattia Furlan | Base resolution DNA methylation data analysis |
methylscaper | Bacher Rhonda | Visualization of Methylation Data |
MethylSeekR | Lukas Burger | Segmentation of Bis-seq data |
methylSig | Raymond G. Cavalcante | MethylSig: Differential Methylation Testing for WGBS and RRBS Data |
methylumi | Sean Davis | Handle Illumina methylation data |
MetID | Zhenzhi Li | Network-based prioritization of putative metabolite IDs |
MetNet | Thomas Naake | Inferring metabolic networks from untargeted high-resolution mass spectrometry data |
mfa | Kieran Campbell | Bayesian hierarchical mixture of factor analyzers for modelling genomic bifurcations |
Mfuzz | Matthias Futschik | Soft clustering of time series gene expression data |
MGFM | Khadija El Amrani | Marker Gene Finder in Microarray gene expression data |
MGFR | Khadija El Amrani | Marker Gene Finder in RNA-seq data |
MGnifyR | Tuomas Borman | R interface to EBI MGnify metagenomics resource |
mgsa | Sebastian Bauer | Model-based gene set analysis |
mia | Tuomas Borman | Microbiome analysis |
miaSim | Yagmur Simsek | Microbiome Data Simulation |
miaViz | Tuomas Borman | Microbiome Analysis Plotting and Visualization |
MiChip | Jonathon Blake | MiChip Parsing and Summarizing Functions |
microbiome | Leo Lahti | Microbiome Analytics |
microbiomeDASim | Justin Williams | Microbiome Differential Abundance Simulation |
microbiomeExplorer | Janina Reeder | Microbiome Exploration App |
microbiomeMarker | Yang Cao | microbiome biomarker analysis toolkit |
MicrobiomeProfiler | Guangchuang Yu | An R/shiny package for microbiome functional enrichment analysis |
MicrobiotaProcess | Shuangbin Xu | A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework |
microRNA | "James F. Reid" | Data and functions for dealing with microRNAs |
microSTASIS | Pedro Sánchez-Sánchez | Microbiota STability ASsessment via Iterative cluStering |
MICSQTL | Qian Li | MICSQTL (Multi-omic deconvolution, Integration and Cell-type-specific Quantitative Trait Loci) |
midasHLA | Maciej Migdał | R package for immunogenomics data handling and association analysis |
miloR | Mike Morgan | Differential neighbourhood abundance testing on a graph |
mimager | Aaron Wolen | mimager: The Microarray Imager |
mina | Rui Guan | Microbial community dIversity and Network Analysis |
MineICA | Anne Biton | Analysis of an ICA decomposition obtained on genomics data |
minet | Patrick E. Meyer | Mutual Information NETworks |
minfi | Kasper Daniel Hansen | Analyze Illumina Infinium DNA methylation arrays |
MinimumDistance | Robert Scharpf | A Package for De Novo CNV Detection in Case-Parent Trios |
MiPP | Sukwoo Kim | Misclassification Penalized Posterior Classification |
miQC | Ariel Hippen | Flexible, probabilistic metrics for quality control of scRNA-seq data |
MIRA | John Lawson | Methylation-Based Inference of Regulatory Activity |
MiRaGE | Y-h. Taguchi | MiRNA Ranking by Gene Expression |
miRBaseConverter | Taosheng Xu Taosheng Xu | A comprehensive and high-efficiency tool for converting and retrieving the information of miRNAs in different miRBase versions |
miRcomp | Matthew N. McCall | Tools to assess and compare miRNA expression estimatation methods |
mirIntegrator | Diana Diaz | Integrating microRNA expression into signaling pathways for pathway analysis |
MIRit | Jacopo Ronchi | Integrate microRNA and gene expression to decipher pathway complexity |
miRLAB | Thuc Duy Le | Dry lab for exploring miRNA-mRNA relationships |
miRNAmeConverter | Stefan J. Haunsberger | Convert miRNA Names to Different miRBase Versions |
miRNApath | James M. Ward | miRNApath: Pathway Enrichment for miRNA Expression Data |
miRNAtap | T. Ian Simpson | miRNAtap: microRNA Targets - Aggregated Predictions |
miRSM | Junpeng Zhang | Inferring miRNA sponge modules in heterogeneous data |
miRspongeR | Junpeng Zhang | Identification and analysis of miRNA sponge regulation |
mirTarRnaSeq | Mercedeh Movassagh | mirTarRnaSeq |
missMethyl | Belinda Phipson, Jovana Maksimovic, Andrew Lonsdale, Calandra Grima | Analysing Illumina HumanMethylation BeadChip Data |
missRows | Gonzalez Ignacio | Handling Missing Individuals in Multi-Omics Data Integration |
mistyR | Jovan Tanevski | Multiview Intercellular SpaTial modeling framework |
mitch | Mark Ziemann | Multi-Contrast Gene Set Enrichment Analysis |
mitoClone2 | Benjamin Story | Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations |
mixOmics | Max Bladen | Omics Data Integration Project |
MLInterfaces | Vincent Carey | Uniform interfaces to R machine learning procedures for data in Bioconductor containers |
MLP | Tobias Verbeke | Mean Log P Analysis |
MLSeq | Gokmen Zararsiz | Machine Learning Interface for RNA-Seq Data |
MMDiff2 | Gabriele Schweikert | Statistical Testing for ChIP-Seq data sets |
MMUPHin | Siyuan MA | Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studies |
mnem | Martin Pirkl | Mixture Nested Effects Models |
moanin | Nelle Varoquaux | An R Package for Time Course RNASeq Data Analysis |
mobileRNA | Katie Jeynes-Cupper | mobileRNA: Investigate the RNA mobilome & population-scale changes |
MODA | Dong Li | MODA: MOdule Differential Analysis for weighted gene co-expression network |
ModCon | Johannes Ptok | Modifying splice site usage by changing the mRNP code, while maintaining the genetic code |
Modstrings | Felix G.M. Ernst | Working with modified nucleotide sequences |
MOFA2 | Ricard Argelaguet | Multi-Omics Factor Analysis v2 |
MOGAMUN | Elva-María Novoa-del-Toro | MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks |
mogsa | Chen Meng | Multiple omics data integrative clustering and gene set analysis |
MoleculeExperiment | Shila Ghazanfar | Prioritising a molecule-level storage of Spatial Transcriptomics Data |
MOMA | Sunny Jones | Multi Omic Master Regulator Analysis |
monaLisa | Michael Stadler | Binned Motif Enrichment Analysis and Visualization |
monocle | Cole Trapnell | Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq |
Moonlight2R | Matteo Tiberti | Identify oncogenes and tumor suppressor genes from omics data |
MoonlightR | Matteo Tiberti | Identify oncogenes and tumor suppressor genes from omics data |
mosaics | Dongjun Chung | MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq) |
mosbi | Tim Daniel Rose | Molecular Signature identification using Biclustering |
mosdef | Federico Marini | MOSt frequently used and useful Differential Expression Functions |
MOSim | Sonia Tarazona | Multi-Omics Simulation (MOSim) |
Motif2Site | Peyman Zarrineh | Detect binding sites from motifs and ChIP-seq experiments, and compare binding sites across conditions |
motifbreakR | Simon Gert Coetzee | A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites |
motifcounter | Wolfgang Kopp | R package for analysing TFBSs in DNA sequences |
MotifDb | Paul Shannon | An Annotated Collection of Protein-DNA Binding Sequence Motifs |
motifmatchr | Alicia Schep | Fast Motif Matching in R |
motifStack | Jianhong Ou | Plot stacked logos for single or multiple DNA, RNA and amino acid sequence |
motifTestR | Stevie Pederson | Perform key tests for binding motifs in sequence data |
MouseFM | Matthias Munz | In-silico methods for genetic finemapping in inbred mice |
MPAC | Peng Liu | Multi-omic Pathway Analysis of Cancer |
MPFE | Conrad Burden | Estimation of the amplicon methylation pattern distribution from bisulphite sequencing data |
mpra | Leslie Myint | Analyze massively parallel reporter assays |
MPRAnalyze | Tal Ashuach | Statistical Analysis of MPRA data |
MQmetrics | Alvaro Sanchez-Villalba | Quality Control of Protemics Data |
msa | Ulrich Bodenhofer | Multiple Sequence Alignment |
MSA2dist | Kristian K Ullrich | MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis |
MsBackendMassbank | RforMassSpectrometry Package Maintainer | Mass Spectrometry Data Backend for MassBank record Files |
MsBackendMgf | RforMassSpectrometry Package Maintainer | Mass Spectrometry Data Backend for Mascot Generic Format (mgf) Files |
MsBackendMsp | Johannes Rainer | Mass Spectrometry Data Backend for NIST msp Files |
MsBackendRawFileReader | Christian Panse | Mass Spectrometry Backend for Reading Thermo Fisher Scientific raw Files |
MsBackendSql | Johannes Rainer | SQL-based Mass Spectrometry Data Backend |
MsCoreUtils | RforMassSpectrometry Package Maintainer | Core Utils for Mass Spectrometry Data |
MsDataHub | Laurent Gatto | Mass Spectrometry Data on ExperimentHub |
MsExperiment | Laurent Gatto | Infrastructure for Mass Spectrometry Experiments |
MsFeatures | Johannes Rainer | Functionality for Mass Spectrometry Features |
msgbsR | Benjamin Mayne | msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions |
msImpute | Soroor Hediyeh-zadeh | Imputation of label-free mass spectrometry peptides |
mslp | Chunxuan Shao | Predict synthetic lethal partners of tumour mutations |
msmsEDA | Josep Gregori | Exploratory Data Analysis of LC-MS/MS data by spectral counts |
msmsTests | Josep Gregori i Font | LC-MS/MS Differential Expression Tests |
MSnbase | Laurent Gatto | Base Functions and Classes for Mass Spectrometry and Proteomics |
MSnID | Vlad Petyuk | Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications |
MSPrep | Max McGrath | Package for Summarizing, Filtering, Imputing, and Normalizing Metabolomics Data |
msPurity | Thomas N. Lawson | Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics |
msqrob2 | Lieven Clement | Robust statistical inference for quantitative LC-MS proteomics |
MsQuality | Thomas Naake | MsQuality - Quality metric calculation from Spectra and MsExperiment objects |
MSstats | Meena Choi | Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments |
MSstatsBig | Mateusz Staniak | MSstats Preprocessing for Larger than Memory Data |
MSstatsConvert | Mateusz Staniak | Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format |
MSstatsLiP | Devon Kohler | LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments |
MSstatsLOBD | Devon Kohler | Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD) |
MSstatsPTM | Devon Kohler | Statistical Characterization of Post-translational Modifications |
MSstatsQC | Eralp Dogu | Longitudinal system suitability monitoring and quality control for proteomic experiments |
MSstatsQCgui | Eralp Dogu | A graphical user interface for MSstatsQC package |
MSstatsShiny | Devon Kohler | MSstats GUI for Statistical Anaylsis of Proteomics Experiments |
MSstatsTMT | Devon Kohler | Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling |
MuData | Danila Bredikhin | Serialization for MultiAssayExperiment Objects |
Mulcom | Claudio Isella | Calculates Mulcom test |
MultiAssayExperiment | Marcel Ramos | Software for the integration of multi-omics experiments in Bioconductor |
MultiBaC | The package maintainer | Multiomic Batch effect Correction |
multiClust | Nathan Lawlor | multiClust: An R-package for Identifying Biologically Relevant Clusters in Cancer Transcriptome Profiles |
multicrispr | Aditya Bhagwat | Multi-locus multi-purpose Crispr/Cas design |
MultiDataSet | Xavier Escrib Montagut | Implementation of MultiDataSet and ResultSet |
multiGSEA | Sebastian Canzler | Combining GSEA-based pathway enrichment with multi omics data integration |
multiHiCcompare | Mikhail Dozmorov | Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available |
MultiMed | Simina M. Boca | Testing multiple biological mediators simultaneously |
multiMiR | Spencer Mahaffey | Integration of multiple microRNA-target databases with their disease and drug associations |
MultimodalExperiment | Lucas Schiffer | Integrative Bulk and Single-Cell Experiment Container |
MultiRNAflow | Rodolphe Loubaton | An R package for integrated analysis of temporal RNA-seq data with multiple biological conditions |
multiscan | Mizanur Khondoker | R package for combining multiple scans |
multistateQTL | Amelia Dunstone | Toolkit for the analysis of multi-state QTL data |
multiWGCNA | Dario Tommasini | multiWGCNA |
multtest | Katherine S. Pollard | Resampling-based multiple hypothesis testing |
mumosa | Aaron Lun | Multi-Modal Single-Cell Analysis Methods |
MungeSumstats | Alan Murphy | Standardise summary statistics from GWAS |
muscat | Helena L. Crowell | Multi-sample multi-group scRNA-seq data analysis tools |
muscle | Alex T. Kalinka | Multiple Sequence Alignment with MUSCLE |
musicatk | Joshua D. Campbell | Mutational Signature Comprehensive Analysis Toolkit |
MutationalPatterns | Mark van Roosmalen | Comprehensive genome-wide analysis of mutational processes |
MVCClass | Elizabeth Whalen | Model-View-Controller (MVC) Classes |
MWASTools | Andrea Rodriguez-Martinez, Rafael Ayala | MWASTools: an integrated pipeline to perform metabolome-wide association studies |
mygene | Adam Mark, Cyrus Afrasiabi, Chunlei Wu | Access MyGene.Info_ services |
myvariant | Adam Mark, Chunlei Wu | Accesses MyVariant.info variant query and annotation services |
mzID | Laurent Gatto | An mzIdentML parser for R |
mzR | Steffen Neumann | parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data) |
NADfinder | Jianhong Ou, Lihua Julie Zhu | Call wide peaks for sequencing data |
NanoMethViz | Shian Su | Visualise methylation data from Oxford Nanopore sequencing |
NanoStringDiff | tingting zhai,hong wang | Differential Expression Analysis of NanoString nCounter Data |
NanoStringNCTools | Maddy Griswold | NanoString nCounter Tools |
nanotatoR | Surajit Bhattacharya | Next generation structural variant annotation and classification |
NanoTube | Caleb Class | An Easy Pipeline for NanoString nCounter Data Analysis |
NBAMSeq | Xu Ren | Negative Binomial Additive Model for RNA-Seq Data |
ncdfFlow | Mike Jiang | ncdfFlow: A package that provides HDF5 based storage for flow cytometry data. |
ncGTW | Chiung-Ting Wu | Alignment of LC-MS Profiles by Neighbor-wise Compound-specific Graphical Time Warping with Misalignment Detection |
NCIgraph | Laurent Jacob | Pathways from the NCI Pathways Database |
ncRNAtools | Lara Selles Vidal | An R toolkit for non-coding RNA |
ndexr | Florian Auer | NDEx R client library |
nearBynding | Veronica Busa | Discern RNA structure proximal to protein binding |
Nebulosa | Jose Alquicira-Hernandez | Single-Cell Data Visualisation Using Kernel Gene-Weighted Density Estimation |
nempi | Martin Pirkl | Inferring unobserved perturbations from gene expression data |
NetActivity | Carlos Ruiz-Arenas | Compute gene set scores from a deep learning framework |
netboost | Pascal Schlosser | Network Analysis Supported by Boosting |
netDx | Shraddha Pai | Network-based patient classifier |
nethet | Nicolas Staedler, Frank Dondelinger | A bioconductor package for high-dimensional exploration of biological network heterogeneity |
netOmics | Antoine Bodein | Multi-Omics (time-course) network-based integration and interpretation |
netprioR | Fabian Schmich | A model for network-based prioritisation of genes |
netresponse | Leo Lahti | Functional Network Analysis |
NetSAM | Zhiao Shi | Network Seriation And Modularization |
netSmooth | Jonathan Ronen | Network smoothing for scRNAseq |
netZooR | Marouen Ben Guebila | Unified methods for the inference and analysis of gene regulatory networks |
NeuCA | Hao Feng | NEUral network-based single-Cell Annotation tool |
NewWave | Federico Agostinis | Negative binomial model for scRNA-seq |
ngsReports | Stevie Pederson | Load FastqQC reports and other NGS related files |
nipalsMCIA | Maximilian Mattessich | Multiple Co-Inertia Analysis via the NIPALS Method |
nnNorm | Adi Laurentiu Tarca | Spatial and intensity based normalization of cDNA microarray data based on robust neural nets |
nnSVG | Lukas M. Weber | Scalable identification of spatially variable genes in spatially-resolved transcriptomics data |
NOISeq | Sonia Tarazona | Exploratory analysis and differential expression for RNA-seq data |
nondetects | Valeriia Sherina | Non-detects in qPCR data |
NoRCE | Gulden Olgun | NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment |
normalize450K | Jonathan Alexander Heiss | Preprocessing of Illumina Infinium 450K data |
NormalyzerDE | Jakob Willforss | Evaluation of normalization methods and calculation of differential expression analysis statistics |
NormqPCR | James Perkins | Functions for normalisation of RT-qPCR data |
normr | Johannes Helmuth | Normalization and difference calling in ChIP-seq data |
NPARC | Nils Kurzawa | Non-parametric analysis of response curves for thermal proteome profiling experiments |
npGSEA | Jessica Larson | Permutation approximation methods for gene set enrichment analysis (non-permutation GSEA) |
NTW | Yuanhua Liu | Predict gene network using an Ordinary Differential Equation (ODE) based method |
nucleoSim | Astrid Deschênes | Generate synthetic nucleosome maps |
nucleR | Alba Sala | Nucleosome positioning package for R |
nuCpos | Hiroaki Kato | An R package for prediction of nucleosome positions |
nullranges | Michael Love | Generation of null ranges via bootstrapping or covariate matching |
NuPoP | Ji-Ping Wang | An R package for nucleosome positioning prediction |
occugene | Oliver Will | Functions for Multinomial Occupancy Distribution |
OCplus | Alexander Ploner | Operating characteristics plus sample size and local fdr for microarray experiments |
octad | E. Chekalin | Open Cancer TherApeutic Discovery (OCTAD) |
odseq | José Jiménez | Outlier detection in multiple sequence alignments |
OGRE | Sven Berres | Calculate, visualize and analyse overlap between genomic regions |
oligo | Benilton Carvalho | Preprocessing tools for oligonucleotide arrays |
oligoClasses | Benilton Carvalho and Robert Scharpf | Classes for high-throughput arrays supported by oligo and crlmm |
OLIN | Matthias Futschik | Optimized local intensity-dependent normalisation of two-color microarrays |
OLINgui | Matthias Futschik | Graphical user interface for OLIN |
omada | Sokratis Kariotis | Machine learning tools for automated transcriptome clustering analysis |
OmaDB | Klara Kaleb, Adrian Altenhoff | R wrapper for the OMA REST API |
omicade4 | Chen Meng | Multiple co-inertia analysis of omics datasets |
OmicCircos | Ying Hu | High-quality circular visualization of omics data |
omicplotR | Daniel Giguere | Visual Exploration of Omic Datasets Using a Shiny App |
omicRexposome | Xavier Escribà Montagut | Exposome and omic data associatin and integration analysis |
OMICsPCA | Subhadeep Das | An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples |
omicsPrint | Davy Cats | Cross omic genetic fingerprinting |
omicsViewer | Chen Meng | Interactive and explorative visualization of SummarizedExperssionSet or ExpressionSet using omicsViewer |
Omixer | Lucy Sinke | Omixer: multivariate and reproducible sample randomization to proactively counter batch effects in omics studies |
OmnipathR | Denes Turei | OmniPath web service client and more |
ompBAM | Alex Chit Hei Wong | C++ Library for OpenMP-based multi-threaded sequential profiling of Binary Alignment Map (BAM) files |
oncomix | Daniel Pique | Identifying Genes Overexpressed in Subsets of Tumors from Tumor-Normal mRNA Expression Data |
oncoscanR | Yann Christinat | Secondary analyses of CNV data (HRD and more) |
OncoScore | Luca De Sano | A tool to identify potentially oncogenic genes |
OncoSimulR | Ramon Diaz-Uriarte | Forward Genetic Simulation of Cancer Progression with Epistasis |
onlineFDR | David S. Robertson | Online error rate control |
ontoProc | Vincent Carey | processing of ontologies of anatomy, cell lines, and so on |
openCyto | Mike Jiang | Hierarchical Gating Pipeline for flow cytometry data |
openPrimeR | Matthias Döring | Multiplex PCR Primer Design and Analysis |
OpenStats | Marina Kan | A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput genotype-phenotype association |
oposSOM | Henry Loeffler-Wirth | Comprehensive analysis of transcriptome data |
oppar | Soroor Hediyeh zadeh | Outlier profile and pathway analysis in R |
oppti | Abdulkadir Elmas | Outlier Protein and Phosphosite Target Identifier |
optimalFlow | Hristo Inouzhe | optimalFlow |
OPWeight | Mohamad Hasan | Optimal p-value weighting with independent information |
OrderedList | Claudio Lottaz | Similarities of Ordered Gene Lists |
ORFhunteR | Vasily V. Grinev | Predict open reading frames in nucleotide sequences |
ORFik | Haakon Tjeldnes | Open Reading Frames in Genomics |
Organism.dplyr | Martin Morgan | dplyr-based Access to Bioconductor Annotation Resources |
OrganismDbi | Bioconductor Package Maintainer | Software to enable the smooth interfacing of different database packages |
orthogene | Brian Schilder | Interspecies gene mapping |
orthos | Panagiotis Papasaikas | `orthos` is an R package for variance decomposition using conditional variational auto-encoders |
OSAT | Li Yan | OSAT: Optimal Sample Assignment Tool |
Oscope | Ning Leng | Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq |
OTUbase | Daniel Beck | Provides structure and functions for the analysis of OTU data |
OUTRIDER | Christian Mertes | OUTRIDER - OUTlier in RNA-Seq fInDER |
OutSplice | Theresa Guo | Comparison of Splicing Events between Tumor and Normal Samples |
OVESEG | Lulu Chen | OVESEG-test to detect tissue/cell-specific markers |
PAA | Michael Turewicz, Martin Eisenacher | PAA (Protein Array Analyzer) |
packFinder | Jack Gisby | de novo Annotation of Pack-TYPE Transposable Elements |
padma | Andrea Rau | Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis |
PADOG | Adi L. Tarca | Pathway Analysis with Down-weighting of Overlapping Genes (PADOG) |
pageRank | Hongxu Ding | Temporal and Multiplex PageRank for Gene Regulatory Network Analysis |
PAIRADISE | Qiang Hu, Levon Demirdjian | PAIRADISE: Paired analysis of differential isoform expression |
paircompviz | Michal Burda | Multiple comparison test visualization |
pairedGSEA | Søren Helweg Dam | Paired DGE and DGS analysis for gene set enrichment analysis |
pairkat | Max McGrath | PaIRKAT |
pandaR | Joseph N. Paulson, Dan Schlauch | PANDA Algorithm |
panelcn.mops | Gundula Povysil | CNV detection tool for targeted NGS panel data |
PanomiR | Pourya Naderi | Detection of miRNAs that regulate interacting groups of pathways |
panp | Peter Warren | Presence-Absence Calls from Negative Strand Matching Probesets |
PANR | Xin Wang | Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations |
PanViz | Luca Anholt | Integrating Multi-Omic Network Data With Summay-Level GWAS Data |
pareg | Kim Philipp Jablonski | Pathway enrichment using a regularized regression approach |
parglms | VJ Carey | support for parallelized estimation of GLMs/GEEs |
parody | Vince Carey | Parametric And Resistant Outlier DYtection |
partCNV | Ziyi Li | Infer locally aneuploid cells using single cell RNA-seq data |
PAST | Thrash Adam | Pathway Association Study Tool (PAST) |
Path2PPI | Oliver Philipp | Prediction of pathway-related protein-protein interaction networks |
pathifier | Assif Yitzhaky | Quantify deregulation of pathways in cancer |
pathlinkR | Travis Blimkie | Analyze and interpret RNA-Seq results |
PathNet | Ludwig Geistlinger | An R package for pathway analysis using topological information |
PathoStat | Solaiappan Manimaran, Yue Zhao | PathoStat Statistical Microbiome Analysis Package |
pathRender | Vince Carey | Render molecular pathways |
pathview | Weijun Luo | a tool set for pathway based data integration and visualization |
pathwayPCA | Gabriel Odom | Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection |
paxtoolsr | Augustin Luna | Access Pathways from Multiple Databases Through BioPAX and Pathway Commons |
pcaExplorer | Federico Marini | Interactive Visualization of RNA-seq Data Using a Principal Components Approach |
pcaMethods | Henning Redestig | A collection of PCA methods |
PCAN | Matthew Page and Patrice Godard | Phenotype Consensus ANalysis (PCAN) |
PCAtools | Kevin Blighe | PCAtools: Everything Principal Components Analysis |
PDATK | Benjamin Haibe-Kains | Pancreatic Ductal Adenocarcinoma Tool-Kit |
pdInfoBuilder | Benilton Carvalho | Platform Design Information Package Builder |
PeacoQC | Annelies Emmaneel | Peak-based selection of high quality cytometry data |
peakPantheR | Arnaud Wolfer | Peak Picking and Annotation of High Resolution Experiments |
PECA | Tomi Suomi | Probe-level Expression Change Averaging |
peco | Chiaowen Joyce Hsiao | A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data |
Pedixplorer | Louis Le Nézet | Pedigree Functions |
pengls | Stijn Hawinkel | Fit Penalised Generalised Least Squares models |
PepSetTest | Junmin Wang | Peptide Set Test |
PepsNMR | Manon Martin | Pre-process 1H-NMR FID signals |
pepStat | Gregory C Imholte | Statistical analysis of peptide microarrays |
pepXMLTab | Xiaojing Wang | Parsing pepXML files and filter based on peptide FDR. |
periodicDNA | Jacques Serizay | Set of tools to identify periodic occurrences of k-mers in DNA sequences |
pfamAnalyzeR | Kristoffer Vitting-Seerup | Identification of domain isotypes in pfam data |
pgca | Gabriela Cohen-Freue | PGCA: An Algorithm to Link Protein Groups Created from MS/MS Data |
pgxRpi | Hangjia Zhao | R wrapper for Progenetix |
phantasus | Alexey Sergushichev | Visual and interactive gene expression analysis |
phantasusLite | Alexey Sergushichev | Loading and annotation RNA-seq counts matrices |
PharmacoGx | Benjamin Haibe-Kains | Analysis of Large-Scale Pharmacogenomic Data |
PhenoGeneRanker | Cagatay Dursun | PhenoGeneRanker: A gene and phenotype prioritization tool |
phenomis | Etienne A. Thevenot | Postprocessing and univariate analysis of omics data |
phenopath | Kieran Campbell | Genomic trajectories with heterogeneous genetic and environmental backgrounds |
phenoTest | Evarist Planet | Tools to test association between gene expression and phenotype in a way that is efficient, structured, fast and scalable. We also provide tools to do GSEA (Gene set enrichment analysis) and copy number variation. |
PhenStat | Hamed Haselimashhadi | Statistical analysis of phenotypic data |
philr | Justin Silverman | Phylogenetic partitioning based ILR transform for metagenomics data |
PhIPData | Athena Chen | Container for PhIP-Seq Experiments |
phosphonormalizer | Sohrab Saraei | Compensates for the bias introduced by median normalization in |
PhosR | Taiyun Kim | A set of methods and tools for comprehensive analysis of phosphoproteomics data |
PhyloProfile | Vinh Tran | PhyloProfile |
phyloseq | Paul J. McMurdie | Handling and analysis of high-throughput microbiome census data |
Pi | Hai Fang | Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level |
piano | Leif Varemo Wigge | Platform for integrative analysis of omics data |
pickgene | Brian S. Yandell | Adaptive Gene Picking for Microarray Expression Data Analysis |
PICS | Renan Sauteraud | Probabilistic inference of ChIP-seq |
Pigengene | Habil Zare | Infers biological signatures from gene expression data |
PING | Renan Sauteraud | Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data |
pipeComp | Pierre-Luc Germain | pipeComp pipeline benchmarking framework |
pipeFrame | Zheng Wei | Pipeline framework for bioinformatics in R |
PIPETS | Quinlan Furumo | Poisson Identification of PEaks from Term-Seq data |
Pirat | Samuel Wieczorek | Precursor or Peptide Imputation under Random Truncation |
PIUMA | Mattia Chiesa | Phenotypes Identification Using Mapper from topological data Analysis |
planet | Victor Yuan | Placental DNA methylation analysis tools |
planttfhunter | Fabrício Almeida-Silva | Identification and classification of plant transcription factors |
plasmut | Adith Arun | Stratifying mutations observed in cell-free DNA and white blood cells as germline, hematopoietic, or somatic |
plgem | Norman Pavelka | Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM) |
plier | Crispin Miller | Implements the Affymetrix PLIER algorithm |
plotgardener | Nicole Kramer, Douglas Phanstiel | Coordinate-Based Genomic Visualization Package for R |
plotGrouper | John D. Gagnon | Shiny app GUI wrapper for ggplot with built-in statistical analysis |
PLPE | Soo-heang Eo | Local Pooled Error Test for Differential Expression with Paired High-throughput Data |
PLSDAbatch | Yiwen (Eva) Wang | PLSDA-batch |
plyinteractions | Jacques Serizay | Extending tidy verbs to genomic interactions |
plyranges | Michael Love | A fluent interface for manipulating GenomicRanges |
pmm | Anna Drewek | Parallel Mixed Model |
pmp | Gavin Rhys Lloyd | Peak Matrix Processing and signal batch correction for metabolomics datasets |
PoDCall | Hans Petter Brodal | Positive Droplet Calling for DNA Methylation Droplet Digital PCR |
podkat | Ulrich Bodenhofer | Position-Dependent Kernel Association Test |
pogos | VJ Carey | PharmacOGenomics Ontology Support |
polyester | Jack Fu, Jeff Leek | Simulate RNA-seq reads |
PolySTest | Veit Schwämmle | PolySTest: Detection of differentially regulated features. Combined statistical testing for data with few replicates and missing values |
POMA | Pol Castellano-Escuder | Tools for Omics Data Analysis |
powerTCR | Hillary Koch | Model-Based Comparative Analysis of the TCR Repertoire |
POWSC | Kenong Su | Simulation, power evaluation, and sample size recommendation for single cell RNA-seq |
ppcseq | Stefano Mangiola | Probabilistic Outlier Identification for RNA Sequencing Generalized Linear Models |
PPInfer | Dongmin Jung | Inferring functionally related proteins using protein interaction networks |
pqsfinder | Jiri Hon | Identification of potential quadruplex forming sequences |
pram | Peng Liu | Pooling RNA-seq datasets for assembling transcript models |
prebs | Karolis Uziela | Probe region expression estimation for RNA-seq data for improved microarray comparability |
preciseTAD | Mikhail Dozmorov | preciseTAD: A machine learning framework for precise TAD boundary prediction |
PREDA | Francesco Ferrari | Position Related Data Analysis |
preprocessCore | Ben Bolstad | A collection of pre-processing functions |
primirTSS | Pumin Li | Prediction of pri-miRNA Transcription Start Site |
PrInCE | Michael Skinnider | Predicting Interactomes from Co-Elution |
proActiv | Joseph Lee | Estimate Promoter Activity from RNA-Seq data |
proBAMr | Xiaojing Wang | Generating SAM file for PSMs in shotgun proteomics data |
PROcess | Xiaochun Li | Ciphergen SELDI-TOF Processing |
procoil | Ulrich Bodenhofer | Prediction of Oligomerization of Coiled Coil Proteins |
proDA | Constantin Ahlmann-Eltze | Differential Abundance Analysis of Label-Free Mass Spectrometry Data |
profileplyr | Tom Carroll, Doug Barrows | Visualization and annotation of read signal over genomic ranges with profileplyr |
profileScoreDist | Paal O. Westermark | Profile score distributions |
progeny | Aurélien Dugourd | Pathway RespOnsive GENes for activity inference from gene expression |
projectR | Genevieve Stein-O'Brien | Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering |
pRoloc | Laurent Gatto | A unifying bioinformatics framework for spatial proteomics |
pRolocGUI | Lisa Breckels | Interactive visualisation of spatial proteomics data |
PROMISE | Stan Pounds, Xueyuan Cao | PRojection Onto the Most Interesting Statistical Evidence |
PROPER | Hao Wu | PROspective Power Evaluation for RNAseq |
PROPS | Lichy Han | PRObabilistic Pathway Score (PROPS) |
Prostar | Samuel Wieczorek | Provides a GUI for DAPAR |
proteinProfiles | Julian Gehring | Protein Profiling |
ProteoDisco | Job van Riet | Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences |
ProteoMM | Yuliya V Karpievitch | Multi-Dataset Model-based Differential Expression Proteomics Analysis Platform |
protGear | Kennedy Mwai | Protein Micro Array Data Management and Interactive Visualization |
ProtGenerics | Laurent Gatto | Generic infrastructure for Bioconductor mass spectrometry packages |
psichomics | Nuno Saraiva-Agostinho | Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation |
PSMatch | Laurent Gatto | Handling and Managing Peptide Spectrum Matches |
psygenet2r | Alba Gutierrez-Sacristan | psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disorders |
ptairMS | camille Roquencourt | Pre-processing PTR-TOF-MS Data |
puma | Xuejun Liu | Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0) |
PureCN | Markus Riester | Copy number calling and SNV classification using targeted short read sequencing |
pvac | Jun Lu, Pierre R. Bushel | PCA-based gene filtering for Affymetrix arrays |
pvca | Jianying LI | Principal Variance Component Analysis (PVCA) |
Pviz | Renan Sauteraud | Peptide Annotation and Data Visualization using Gviz |
pwalign | Hervé Pagès | Perform pairwise sequence alignments |
PWMEnrich | Diego Diez | PWM enrichment analysis |
qckitfastq | August Guang | FASTQ Quality Control |
qcmetrics | Laurent Gatto | A Framework for Quality Control |
QDNAseq | Daoud Sie | Quantitative DNA Sequencing for Chromosomal Aberrations |
QFeatures | Laurent Gatto | Quantitative features for mass spectrometry data |
qmtools | Jaehyun Joo | Quantitative Metabolomics Data Processing Tools |
qpcrNorm | Jessica Mar | Data-driven normalization strategies for high-throughput qPCR data. |
qpgraph | Robert Castelo | Estimation of genetic and molecular regulatory networks from high-throughput genomics data |
qPLEXanalyzer | Ashley Sawle | Tools for quantitative proteomics data analysis |
qsea | Matthias Lienhard | IP-seq data analysis and vizualization |
qsmooth | Stephanie C. Hicks | Smooth quantile normalization |
QSutils | Mercedes Guerrero-Murillo | Quasispecies Diversity |
qsvaR | Hedia Tnani | Generate Quality Surrogate Variable Analysis for Degradation Correction |
QTLExperiment | Amelia Dunstone | S4 classes for QTL summary statistics and metadata |
Qtlizer | Matthias Munz | Comprehensive QTL annotation of GWAS results |
quantiseqr | Federico Marini | Quantification of the Tumor Immune contexture from RNA-seq data |
quantro | Stephanie Hicks | A test for when to use quantile normalization |
quantsmooth | Jan Oosting | Quantile smoothing and genomic visualization of array data |
QuartPAC | Gregory Ryslik | Identification of mutational clusters in protein quaternary structures |
QuasR | Michael Stadler | Quantify and Annotate Short Reads in R |
QuaternaryProd | Carl Tony Fakhry | Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs |
QUBIC | Yu Zhang | An R package for qualitative biclustering in support of gene co-expression analyses |
qusage | Christopher Bolen | qusage: Quantitative Set Analysis for Gene Expression |
qvalue | John D. Storey, Andrew J. Bass | Q-value estimation for false discovery rate control |
R3CPET | Mohamed Nadhir Djekidel | 3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process |
r3Cseq | Supat Thongjuea or | Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq) |
R453Plus1Toolbox | Hans-Ulrich Klein | A package for importing and analyzing data from Roche's Genome Sequencer System |
R4RNA | Daniel Lai | An R package for RNA visualization and analysis |
RadioGx | Benjamin Haibe-Kains | Analysis of Large-Scale Radio-Genomic Data |
raer | Kent Riemondy | RNA editing tools in R |
RaggedExperiment | Marcel Ramos | Representation of Sparse Experiments and Assays Across Samples |
RAIDS | Pascal Belleau | Accurate Inference of Genetic Ancestry from Cancer Sequences |
rain | Paul F. Thaben | Rhythmicity Analysis Incorporating Non-parametric Methods |
ramr | Oleksii Nikolaienko | Detection of Rare Aberrantly Methylated Regions in Array and NGS Data |
ramwas | Andrey A Shabalin | Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms |
RandomWalkRestartMH | Alberto Valdeolivas | Random walk with restart on multiplex and heterogeneous Networks |
randPack | Robert Gentleman | Randomization routines for Clinical Trials |
randRotation | Peter Hettegger | Random Rotation Methods for High Dimensional Data with Batch Structure |
RankProd | Francesco Del Carratore | Rank Product method for identifying differentially expressed genes with application in meta-analysis |
RAREsim | Ryan Barnard | Simulation of Rare Variant Genetic Data |
RareVariantVis | Tomasz Stokowy | A suite for analysis of rare genomic variants in whole genome sequencing data |
Rarr | Mike Smith | Read Zarr Files in R |
rawDiag | Christian Panse | Brings Orbitrap Mass Spectrometry Data to Life; Fast and Colorful |
rawrr | Christian Panse | Direct Access to Orbitrap Data and Beyond |
RbcBook1 | Vince Carey | Support for Springer monograph on Bioconductor |
Rbec | Pengfan Zhang | Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities |
RBGL | Bioconductor Package Maintainer | An interface to the BOOST graph library |
RBioFormats | Andrzej Oleś | R interface to Bio-Formats |
RBioinf | Robert Gentleman | RBioinf |
rBiopaxParser | Frank Kramer | Parses BioPax files and represents them in R |
rBLAST | Michael Hahsler | R Interface for the Basic Local Alignment Search Tool |
RBM | Dongmei Li | RBM: a R package for microarray and RNA-Seq data analysis |
Rbowtie | Michael Stadler | R bowtie wrapper |
Rbowtie2 | Zheng Wei | An R Wrapper for Bowtie2 and AdapterRemoval |
rbsurv | Soo-heang Eo | Robust likelihood-based survival modeling with microarray data |
Rbwa | Jean-Philippe Fortin | R wrapper for BWA-backtrack and BWA-MEM aligners |
RCAS | Bora Uyar | RNA Centric Annotation System |
RCASPAR | Douaa Mugahid, Lars Kaderali | A package for survival time prediction based on a piecewise baseline hazard Cox regression model. |
rcellminer | Augustin Luna, Vinodh Rajapakse, Fathi Elloumi | rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines |
rCGH | Frederic Commo | Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data |
RcisTarget | Gert Hulselmans | RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions |
RCM | Stijn Hawinkel | Fit row-column association models with the negative binomial distribution for the microbiome |
Rcollectl | Vincent Carey | Help use collectl with R in Linux, to measure resource consumption in R processes |
Rcpi | Nan Xiao | Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery |
RCSL | Qinglin Mei | Rank Constrained Similarity Learning for single cell RNA sequencing data |
Rcwl | Qiang Hu | An R interface to the Common Workflow Language |
RcwlPipelines | Qiang Hu | Bioinformatics pipelines based on Rcwl |
RCX | Florian Auer | R package implementing the Cytoscape Exchange (CX) format |
RCy3 | Alex Pico | Functions to Access and Control Cytoscape |
RCyjs | Paul Shannon | Display and manipulate graphs in cytoscape.js |
rDGIdb | Lars Bosshard | R Wrapper for DGIdb |
Rdisop | Steffen Neumann | Decomposition of Isotopic Patterns |
RDRToolbox | Christoph Bartenhagen | A package for nonlinear dimension reduction with Isomap and LLE. |
ReactomeContentService4R | Chi-Lam Poon | Interface for the Reactome Content Service |
ReactomeGraph4R | Chi-Lam Poon | Interface for the Reactome Graph Database |
ReactomeGSA | Johannes Griss | Client for the Reactome Analysis Service for comparative multi-omics gene set analysis |
ReactomePA | Guangchuang Yu | Reactome Pathway Analysis |
ReadqPCR | James Perkins | Read qPCR data |
REBET | Bill Wheeler | The subREgion-based BurdEn Test (REBET) |
rebook | Aaron Lun | Re-using Content in Bioconductor Books |
receptLoss | Daniel Pique | Unsupervised Identification of Genes with Expression Loss in Subsets of Tumors |
reconsi | Stijn Hawinkel | Resampling Collapsed Null Distributions for Simultaneous Inference |
recount | Leonardo Collado-Torres | Explore and download data from the recount project |
recount3 | Leonardo Collado-Torres | Explore and download data from the recount3 project |
recountmethylation | Sean K Maden | Access and analyze public DNA methylation array data compilations |
recoup | Panagiotis Moulos | An R package for the creation of complex genomic profile plots |
RedeR | Mauro Castro | Interactive visualization and manipulation of nested networks |
RedisParam | Martin Morgan | Provide a 'redis' back-end for BiocParallel |
REDseq | Lihua Julie Zhu | Analysis of high-throughput sequencing data processed by restriction enzyme digestion |
RegEnrich | Weiyang Tao | Gene regulator enrichment analysis |
regionalpcs | Tiffany Eulalio | Summarizing Regional Methylation with Regional Principal Components Analysis |
RegionalST | Ziyi Li | Investigating regions of interest and performing cross-regional analysis with spatial transcriptomics data |
regioneR | Bernat Gel | Association analysis of genomic regions based on permutation tests |
regioneReloaded | Roberto Malinverni | RegioneReloaded: Multiple Association for Genomic Region Sets |
regionReport | Leonardo Collado-Torres | Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results |
regsplice | Lukas M. Weber | L1-regularization based methods for detection of differential splicing |
regutools | Joselyn Chavez | regutools: an R package for data extraction from RegulonDB |
REMP | Yinan Zheng | Repetitive Element Methylation Prediction |
Repitools | Mark Robinson | Epigenomic tools |
ReportingTools | Jason A. Hackney, Gabriel Becker, Jessica L. Larson | Tools for making reports in various formats |
RepViz | Thomas Faux, Asta Laiho | Replicate oriented Visualization of a genomic region |
ResidualMatrix | Aaron Lun | Creating a DelayedMatrix of Regression Residuals |
RESOLVE | Luca De Sano | RESOLVE: An R package for the efficient analysis of mutational signatures from cancer genomes |
retrofit | Adam Park | RETROFIT: Reference-free deconvolution of cell mixtures in spatial transcriptomics |
ReUseData | Qian Liu | Reusable and reproducible Data Management |
rexposome | Xavier Escribà Montagut | Exposome exploration and outcome data analysis |
rfaRm | Lara Selles Vidal, Rafael Ayala | An R interface to the Rfam database |
Rfastp | Thomas Carroll | An Ultra-Fast and All-in-One Fastq Preprocessor (Quality Control, Adapter, low quality and polyX trimming) and UMI Sequence Parsing). |
rfPred | Hugo Varet | Assign rfPred functional prediction scores to a missense variants list |
rGADEM | Arnaud Droit | de novo motif discovery |
rGenomeTracks | Omar Elashkar | Integerated visualization of epigenomic data |
RGMQL | Simone Pallotta | GenoMetric Query Language for R/Bioconductor |
RgnTX | Yue Wang | Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity |
rgoslin | Nils Hoffmann | Lipid Shorthand Name Parsing and Normalization |
RGraph2js | Stephane Cano | Convert a Graph into a D3js Script |
Rgraphviz | Kasper Daniel Hansen | Provides plotting capabilities for R graph objects |
rGREAT | Zuguang Gu | GREAT Analysis - Functional Enrichment on Genomic Regions |
RGSEA | Chengcheng Ma | Random Gene Set Enrichment Analysis |
rgsepd | Karl Stamm | Gene Set Enrichment / Projection Displays |
rhdf5 | Mike Smith | R Interface to HDF5 |
rhdf5client | Vincent Carey | Access HDF5 content from HDF Scalable Data Service |
rhdf5filters | Mike Smith | HDF5 Compression Filters |
Rhdf5lib | Mike Smith | hdf5 library as an R package |
Rhisat2 | Charlotte Soneson | R Wrapper for HISAT2 Aligner |
Rhtslib | Hervé Pagès | HTSlib high-throughput sequencing library as an R package |
RiboCrypt | Michal Swirski | Interactive visualization in genomics |
RiboDiPA | Ji-Ping Wang | Differential pattern analysis for Ribo-seq data |
RiboProfiling | A. Popa | Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation |
ribor | Michael Geng | An R Interface for Ribo Files |
riboSeqR | Samuel Granjeaud | Analysis of sequencing data from ribosome profiling experiments |
ribosomeProfilingQC | Jianhong Ou | Ribosome Profiling Quality Control |
rifi | Jens Georg | 'rifi' analyses data from rifampicin time series created by microarray or RNAseq |
rifiComparative | Loubna Youssar | 'rifiComparative' compares the output of rifi from two different conditions. |
RImmPort | Zicheng Hu, Ravi Shankar | RImmPort: Enabling Ready-for-analysis Immunology Research Data |
Risa | Alejandra Gonzalez-Beltran | Converting experimental metadata from ISA-tab into Bioconductor data structures |
RITAN | Michael Zimmermann | Rapid Integration of Term Annotation and Network resources |
RIVER | Yungil Kim | R package for RIVER (RNA-Informed Variant Effect on Regulation) |
RJMCMCNucleosomes | Astrid Deschênes | Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq) |
RLassoCox | Wei Liu | A reweighted Lasso-Cox by integrating gene interaction information |
RLMM | Nusrat Rabbee | A Genotype Calling Algorithm for Affymetrix SNP Arrays |
Rmagpie | Camille Maumet | MicroArray Gene-expression-based Program In Error rate estimation |
RMassBank | RMassBank at Eawag | Workflow to process tandem MS files and build MassBank records |
rmelting | J. Aravind | R Interface to MELTING 5 |
Rmmquant | Zytnicki Matthias | RNA-Seq multi-mapping Reads Quantification Tool |
rmspc | Meriem Bahda | Multiple Sample Peak Calling |
RNAAgeCalc | Xu Ren | A multi-tissue transcriptional age calculator |
RNAdecay | Reed Sorenson | Maximum Likelihood Decay Modeling of RNA Degradation Data |
rnaEditr | Lanyu Zhang | Statistical analysis of RNA editing sites and hyper-editing regions |
RNAinteract | Mike Smith | Estimate Pairwise Interactions from multidimensional features |
RNAmodR | Felix G.M. Ernst | Detection of post-transcriptional modifications in high throughput sequencing data |
RNAmodR.AlkAnilineSeq | Felix G.M. Ernst | Detection of m7G, m3C and D modification by AlkAnilineSeq |
RNAmodR.ML | Felix G.M. Ernst | Detecting patterns of post-transcriptional modifications using machine learning |
RNAmodR.RiboMethSeq | Felix G.M. Ernst | Detection of 2'-O methylations by RiboMethSeq |
RNAsense | Marcus Rosenblatt | Analysis of Time-Resolved RNA-Seq Data |
rnaseqcomp | Mingxiang Teng | Benchmarks for RNA-seq Quantification Pipelines |
RNAseqCovarImpute | Brennan Baker | Impute Covariate Data in RNA Sequencing Studies |
RNASeqPower | Terry M Therneau | Sample size for RNAseq studies |
RnaSeqSampleSize | Shilin Zhao Developer | RnaSeqSampleSize |
RnBeads | Fabian Mueller | RnBeads |
Rnits | Dipen P. Sangurdekar | R Normalization and Inference of Time Series data |
roar | Elena Grassi | Identify differential APA usage from RNA-seq alignments |
roastgsa | Adria Caballe | Rotation based gene set analysis |
ROC | Vince Carey | utilities for ROC, with microarray focus |
ROCpAI | Juan-Pedro Garcia | Receiver Operating Characteristic Partial Area Indexes for evaluating classifiers |
RolDE | Medical Bioinformatics Centre | RolDE: Robust longitudinal Differential Expression |
rols | Laurent Gatto | An R interface to the Ontology Lookup Service |
ROntoTools | Sorin Draghici | R Onto-Tools suite |
ropls | Etienne A. Thevenot | PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data |
ROSeq | Krishan Gupta | Modeling expression ranks for noise-tolerant differential expression analysis of scRNA-Seq data |
ROTS | Tomi Suomi | Reproducibility-Optimized Test Statistic |
RPA | Leo Lahti | RPA: Robust Probabilistic Averaging for probe-level analysis |
rprimer | Sofia Persson | Design Degenerate Oligos from a Multiple DNA Sequence Alignment |
RProtoBufLib | Mike Jiang | C++ headers and static libraries of Protocol buffers |
rpx | Laurent Gatto | R Interface to the ProteomeXchange Repository |
Rqc | Welliton Souza | Quality Control Tool for High-Throughput Sequencing Data |
rqt | Ilya Zhbannikov | rqt: utilities for gene-level meta-analysis |
rqubic | Jitao David Zhang | Qualitative biclustering algorithm for expression data analysis in R |
rRDP | Michael Hahsler | Interface to the RDP Classifier |
RRHO | Jonathan Rosenblatt | Inference on agreement between ordered lists |
rrvgo | Sergi Sayols | Reduce + Visualize GO |
Rsamtools | Bioconductor Package Maintainer | Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import |
rsbml | Michael Lawrence | R support for SBML, using libsbml |
rScudo | Matteo Ciciani | Signature-based Clustering for Diagnostic Purposes |
rsemmed | Leslie Myint | An interface to the Semantic MEDLINE database |
RSeqAn | August Guang | R SeqAn |
Rsubread | Wei Shi, Yang Liao and Gordon K Smyth | Mapping, quantification and variant analysis of sequencing data |
RSVSim | Christoph Bartenhagen | RSVSim: an R/Bioconductor package for the simulation of structural variations |
rSWeeP | Camila P Perico | Spaced Words Projection (SWeeP) |
RTCA | Jitao David Zhang | Open-source toolkit to analyse data from xCELLigence System (RTCA) |
RTCGA | Marcin Kosinski | The Cancer Genome Atlas Data Integration |
RTCGAToolbox | Marcel Ramos | A new tool for exporting TCGA Firehose data |
RTN | Mauro Castro | RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons |
RTNduals | Mauro Castro, Clarice Groeneveld | Analysis of co-regulation and inference of 'dual regulons' |
RTNsurvival | Clarice Groeneveld, Mauro A. A. Castro | Survival analysis using transcriptional networks inferred by the RTN package |
RTopper | Luigi Marchionni | This package is designed to perform Gene Set Analysis across multiple genomic platforms |
Rtpca | Nils Kurzawa | Thermal proximity co-aggregation with R |
rtracklayer | Michael Lawrence | R interface to genome annotation files and the UCSC genome browser |
Rtreemix | Jasmina Bogojeska | Rtreemix: Mutagenetic trees mixture models. |
rTRM | Diego Diez | Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks |
rTRMui | Diego Diez | A shiny user interface for rTRM |
runibic | Patryk Orzechowski | runibic: row-based biclustering algorithm for analysis of gene expression data in R |
RUVcorr | Saskia Freytag | Removal of unwanted variation for gene-gene correlations and related analysis |
RUVnormalize | Laurent Jacob | RUV for normalization of expression array data |
RUVSeq | Davide Risso | Remove Unwanted Variation from RNA-Seq Data |
Rvisdiff | David Barrios | Interactive Graphs for Differential Expression |
RVS | Alexandre Bureau | Computes estimates of the probability of related individuals sharing a rare variant |
rWikiPathways | Egon Willighagen | rWikiPathways - R client library for the WikiPathways API |
S4Arrays | Hervé Pagès | Foundation of array-like containers in Bioconductor |
S4Vectors | Hervé Pagès | Foundation of vector-like and list-like containers in Bioconductor |
safe | Ludwig Geistlinger | Significance Analysis of Function and Expression |
sagenhaft | Tim Beissbarth | Collection of functions for reading and comparing SAGE libraries |
SAIGEgds | Xiuwen Zheng | Scalable Implementation of Generalized mixed models using GDS files in Phenome-Wide Association Studies |
sampleClassifier | Khadija El Amrani | Sample Classifier |
SamSPECTRAL | Habil | Identifies cell population in flow cytometry data |
sangeranalyseR | Kuan-Hao Chao | sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R |
sangerseqR | Jonathon Hill | Tools for Sanger Sequencing Data in R |
SANTA | Alex Cornish | Spatial Analysis of Network Associations |
SARC | Krutik Patel | Statistical Analysis of Regions with CNVs |
sarks | Dennis Wylie | Suffix Array Kernel Smoothing for discovery of correlative sequence motifs and multi-motif domains |
saseR | Alexandre Segers | Scalable Aberrant Splicing and Expression Retrieval |
satuRn | Jeroen Gilis | Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications |
SBGNview | Weijun Luo | "SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways" |
SBMLR | Tomas Radivoyevitch | SBML-R Interface and Analysis Tools |
SC3 | Vladimir Kiselev | Single-Cell Consensus Clustering |
Scale4C | Carolin Walter | Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data |
ScaledMatrix | Aaron Lun | Creating a DelayedMatrix of Scaled and Centered Values |
SCAN.UPC | Stephen R. Piccolo | Single-channel array normalization (SCAN) and Universal exPression Codes (UPC) |
scanMiR | Pierre-Luc Germain | scanMiR |
scanMiRApp | Pierre-Luc Germain | scanMiR shiny application |
scAnnotatR | Johannes Griss | Pretrained learning models for cell type prediction on single cell RNA-sequencing data |
SCANVIS | Phaedra Agius | SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions |
SCArray | Xiuwen Zheng | Large-scale single-cell omics data manipulation with GDS files |
SCArray.sat | Xiuwen Zheng | Large-scale single-cell RNA-seq data analysis using GDS files and Seurat |
scater | Alan O'Callaghan | Single-Cell Analysis Toolkit for Gene Expression Data in R |
scatterHatch | Atul Deshpande | Creates hatched patterns for scatterplots |
scBFA | Ruoxin Li | A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA-seq |
SCBN | Yan Zhou | A statistical normalization method and differential expression analysis for RNA-seq data between different species |
scBubbletree | Simo Kitanovski | Quantitative visual exploration of scRNA-seq data |
scCB2 | Zijian Ni | CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data |
scClassify | Yingxin Lin | scClassify: single-cell Hierarchical Classification |
sccomp | Stefano Mangiola | Robust Outlier-aware Estimation of Composition and Heterogeneity for Single-cell Data |
scDataviz | Kevin Blighe | scDataviz: single cell dataviz and downstream analyses |
scDblFinder | Pierre-Luc Germain | scDblFinder |
scDD | Keegan Korthauer | Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions |
scDDboost | Xiuyu Ma | A compositional model to assess expression changes from single-cell rna-seq data |
scde | Evan Biederstedt | Single Cell Differential Expression |
scDesign3 | Dongyuan Song | A unified framework of realistic in silico data generation and statistical model inference for single-cell and spatial omics |
scDiagnostics | Anthony Christidis | Cell type annotation diagnostics |
scDotPlot | Benjamin I Laufer | Cluster a Single-cell RNA-seq Dot Plot |
scds | Dennis Kostka | In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data |
SCFA | Duc Tran | SCFA: Subtyping via Consensus Factor Analysis |
scFeatureFilter | Guillaume Devailly | A correlation-based method for quality filtering of single-cell RNAseq data |
scFeatures | Yue Cao | scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction |
scGPS | Quan Nguyen | A complete analysis of single cell subpopulations, from identifying subpopulations to analysing their relationship (scGPS = single cell Global Predictions of Subpopulation) |
schex | Saskia Freytag | Hexbin plots for single cell omics data |
scHOT | Shila Ghazanfar | single-cell higher order testing |
scider | Yunshun Chen | Spatial cell-type inter-correlation by density in R |
scifer | Rodrigo Arcoverde Cerveira | Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences |
scmap | Vladimir Kiselev | A tool for unsupervised projection of single cell RNA-seq data |
scMerge | Yingxin Lin | scMerge: Merging multiple batches of scRNA-seq data |
scMET | Andreas C. Kapourani | Bayesian modelling of cell-to-cell DNA methylation heterogeneity |
scmeth | Divy Kangeyan | Functions to conduct quality control analysis in methylation data |
scMitoMut | Wenjie Sun | Single-cell Mitochondrial Mutation Analysis Tool |
scMultiSim | Hechen Li | Simulation of Multi-Modality Single Cell Data Guided By Gene Regulatory Networks and Cell-Cell Interactions |
SCnorm | Rhonda Bacher | Normalization of single cell RNA-seq data |
scone | Davide Risso | Single Cell Overview of Normalized Expression data |
Sconify | Tyler J Burns | A toolkit for performing KNN-based statistics for flow and mass cytometry data |
SCOPE | Rujin Wang | A normalization and copy number estimation method for single-cell DNA sequencing |
scoreInvHap | Dolors Pelegri-Siso | Get inversion status in predefined regions |
scp | Christophe Vanderaa | Mass Spectrometry-Based Single-Cell Proteomics Data Analysis |
scPCA | Philippe Boileau | Sparse Contrastive Principal Component Analysis |
scPipe | Shian Su | Pipeline for single cell multi-omic data pre-processing |
scran | Aaron Lun | Methods for Single-Cell RNA-Seq Data Analysis |
scReClassify | Taiyun Kim | scReClassify: post hoc cell type classification of single-cell RNA-seq data |
scRecover | Zhun Miao | scRecover for imputation of single-cell RNA-seq data |
screenCounter | Aaron Lun | Counting Reads in High-Throughput Sequencing Screens |
ScreenR | Emanuel Michele Soda | Package to Perform High Throughput Biological Screening |
scRepertoire | Nick Borcherding | A toolkit for single-cell immune receptor profiling |
scRNAseqApp | Jianhong Ou | A single-cell RNAseq Shiny app-package |
scruff | Zhe Wang | Single Cell RNA-Seq UMI Filtering Facilitator (scruff) |
scry | Kelly Street | Small-Count Analysis Methods for High-Dimensional Data |
scShapes | Malindrie Dharmaratne | A Statistical Framework for Modeling and Identifying Differential Distributions in Single-cell RNA-sequencing Data |
scTensor | Koki Tsuyuzaki | Detection of cell-cell interaction from single-cell RNA-seq dataset by tensor decomposition |
scTGIF | Koki Tsuyuzaki | Cell type annotation for unannotated single-cell RNA-Seq data |
scTHI | Michele Ceccarelli | Indentification of significantly activated ligand-receptor interactions across clusters of cells from single-cell RNA sequencing data |
scTreeViz | Jayaram Kancherla | R/Bioconductor package to interactively explore and visualize single cell RNA-seq datasets with hierarhical annotations |
scuttle | Aaron Lun | Single-Cell RNA-Seq Analysis Utilities |
scviR | Vincent Carey | experimental inferface from R to scvi-tools |
SDAMS | Yuntong Li | Differential Abundant/Expression Analysis for Metabolomics, Proteomics and single-cell RNA sequencing Data |
seahtrue | Vincent de Boer | Seahtrue revives XF data for structured data analysis |
sechm | Pierre-Luc Germain | sechm: Complex Heatmaps from a SummarizedExperiment |
segmenter | Mahmoud Ahmed | Perform Chromatin Segmentation Analysis in R by Calling ChromHMM |
segmentSeq | Samuel Granjeaud | Methods for identifying small RNA loci from high-throughput sequencing data |
selectKSigs | Zhi Yang | Selecting the number of mutational signatures using a perplexity-based measure and cross-validation |
SELEX | Harmen J. Bussemaker | Functions for analyzing SELEX-seq data |
SemDist | Ian Gonzalez | Information Accretion-based Function Predictor Evaluation |
semisup | Armin Rauschenberger | Semi-Supervised Mixture Model |
seq.hotSPOT | Sydney Grant | Targeted sequencing panel design based on mutation hotspots |
seq2pathway | Arjun Kinstlick | a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data |
seqArchR | Sarvesh Nikumbh | Identify Different Architectures of Sequence Elements |
seqArchRplus | Sarvesh Nikumbh | Downstream analyses of promoter sequence architectures and HTML report generation |
SeqArray | Xiuwen Zheng | Data Management of Large-Scale Whole-Genome Sequence Variant Calls |
seqCAT | Erik Fasterius | High Throughput Sequencing Cell Authentication Toolkit |
seqcombo | Guangchuang Yu | Visualization Tool for Genetic Reassortment |
SeqGate | Stéphanie Rialle | Filtering of Lowly Expressed Features |
SeqGSEA | Xi Wang | Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing |
seqLogo | Robert Ivanek | Sequence logos for DNA sequence alignments |
seqPattern | Vanja Haberle | Visualising oligonucleotide patterns and motif occurrences across a set of sorted sequences |
seqsetvis | Joseph R Boyd | Set Based Visualizations for Next-Gen Sequencing Data |
SeqSQC | Qian Liu | A bioconductor package for sample quality check with next generation sequencing data |
seqTools | Wolfgang Kaisers | Analysis of nucleotide, sequence and quality content on fastq files |
SeqVarTools | Stephanie M. Gogarten | Tools for variant data |
sesame | Wanding Zhou | SEnsible Step-wise Analysis of DNA MEthylation BeadChips |
SEtools | Pierre-Luc Germain | SEtools: tools for working with SummarizedExperiment |
sevenbridges | Phil Webster | Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R |
sevenC | Jonas Ibn-Salem | Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs |
SGCP | Niloofar AghaieAbiane | SGCP: A semi-supervised pipeline for gene clustering using self-training approach in gene co-expression networks |
SGSeq | Leonard Goldstein | Splice event prediction and quantification from RNA-seq data |
SharedObject | Jiefei Wang | Sharing R objects across multiple R processes without memory duplication |
shiny.gosling | Appsilon | A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization for R and Shiny |
shinyepico | Octavio Morante-Palacios | ShinyÉPICo |
shinyMethyl | Jean-Philippe Fortin | Interactive visualization for Illumina methylation arrays |
ShortRead | Bioconductor Package Maintainer | FASTQ input and manipulation |
SIAMCAT | Jakob Wirbel | Statistical Inference of Associations between Microbial Communities And host phenoTypes |
SICtools | Xiaobin Xing | Find SNV/Indel differences between two bam files with near relationship |
SigCheck | Rory Stark | Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadata |
sigFeature | Pijush Das Developer | sigFeature: Significant feature selection using SVM-RFE & t-statistic |
SigFuge | Patrick Kimes | SigFuge |
siggenes | Holger Schwender | Multiple Testing using SAM and Efron's Empirical Bayes Approaches |
sights | Elika Garg | Statistics and dIagnostic Graphs for HTS |
signatureSearch | Brendan Gongol | Environment for Gene Expression Searching Combined with Functional Enrichment Analysis |
signeR | Renan Valieris | Empirical Bayesian approach to mutational signature discovery |
signifinder | Stefania Pirrotta | Collection and implementation of public transcriptional cancer signatures |
SigsPack | Franziska Schumann | Mutational Signature Estimation for Single Samples |
sigsquared | UnJin Lee | Gene signature generation for functionally validated signaling pathways |
SIM | Renee X. de Menezes | Integrated Analysis on two human genomic datasets |
SIMAT | M. R. Nezami Ranjbar | GC-SIM-MS data processing and alaysis tool |
SimBu | Alexander Dietrich | Simulate Bulk RNA-seq Datasets from Single-Cell Datasets |
SIMD | Jiadi Zhu | Statistical Inferences with MeDIP-seq Data (SIMD) to infer the methylation level for each CpG site |
SimFFPE | Lanying Wei | NGS Read Simulator for FFPE Tissue |
similaRpeak | Astrid Deschênes | Metrics to estimate a level of similarity between two ChIP-Seq profiles |
SIMLR | Luca De Sano | Single-cell Interpretation via Multi-kernel LeaRning (SIMLR) |
simona | Zuguang Gu | Semantic Similarity on Bio-Ontologies |
simPIC | Sagrika Chugh | simPIC: flexible simulation of paired-insertion counts for single-cell ATAC-sequencing data |
simpleSeg | Ellis Patrick | A package to perform simple cell segmentation |
simplifyEnrichment | Zuguang Gu | Simplify Functional Enrichment Results |
sincell | Miguel Julia, Antonio Rausell | R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data |
single | Rocio Espada | Accurate consensus sequence from nanopore reads of a gene library |
SingleCellAlleleExperiment | Jonas Schuck | S4 Class for Single Cell Data with Allele and Functional Levels for Immune Genes |
SingleCellExperiment | Davide Risso | S4 Classes for Single Cell Data |
SingleCellSignalR | Jacques Colinge Developer | Cell Signalling Using Single Cell RNAseq Data Analysis |
singleCellTK | Joshua David Campbell | Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data |
SingleMoleculeFootprinting | Guido Barzaghi | Analysis tools for Single Molecule Footprinting (SMF) data |
SingleR | Aaron Lun | Reference-Based Single-Cell RNA-Seq Annotation |
singscore | Malvika Kharbanda | Rank-based single-sample gene set scoring method |
SiPSiC | Daniel Davis | Calculate Pathway Scores for Each Cell in scRNA-Seq Data |
sitadela | Panagiotis Moulos | An R package for the easy provision of simple but complete tab-delimited genomic annotation from a variety of sources and organisms |
sitePath | Chengyang Ji | Phylogeny-based sequence clustering with site polymorphism |
sizepower | Weiliang Qiu | Sample Size and Power Calculation in Micorarray Studies |
sketchR | Charlotte Soneson | An R interface for python subsampling/sketching algorithms |
skewr | Ryan Putney | Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip |
slalom | Davis McCarthy | Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data |
slingshot | Kelly Street | Tools for ordering single-cell sequencing |
SLqPCR | Matthias Kohl | Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH |
SMAD | Qingzhou Zhang | Statistical Modelling of AP-MS Data (SMAD) |
smartid | Jinjin Chen | Scoring and Marker Selection Method Based on Modified TF-IDF |
SMITE | Neil Ari Wijetunga, Andrew Damon Johnston | Significance-based Modules Integrating the Transcriptome and Epigenome |
smoothclust | Lukas M. Weber | smoothclust |
SNAGEE | David Venet | Signal-to-Noise applied to Gene Expression Experiments |
snapcount | Rone Charles | R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts |
snifter | Alan O'Callaghan | R wrapper for the python openTSNE library |
snm | John D. Storey | Supervised Normalization of Microarrays |
SNPediaR | David Montaner | Query data from SNPedia |
SNPhood | Christian Arnold | SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data |
SNPRelate | Xiuwen Zheng | Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data |
snpStats | David Clayton | SnpMatrix and XSnpMatrix classes and methods |
soGGi | Tom Carroll | Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots Summarised Over Grouped Genomic Intervals |
SomaticSignatures | Julian Gehring | Somatic Signatures |
SOMNiBUS | Kathleen Klein | Smooth modeling of bisulfite sequencing |
SpaceMarkers | Atul Deshpande | Spatial Interaction Markers |
SpacePAC | Gregory Ryslik | Identification of Mutational Clusters in 3D Protein Space via Simulation. |
Spaniel | Rachel Queen | Spatial Transcriptomics Analysis |
sparrow | Steve Lianoglou | Take command of set enrichment analyses through a unified interface |
SparseArray | Hervé Pagès | High-performance sparse data representation and manipulation in R |
sparseMatrixStats | Constantin Ahlmann-Eltze | Summary Statistics for Rows and Columns of Sparse Matrices |
sparsenetgls | Irene Zeng | Using Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regression |
SparseSignatures | Luca De Sano | SparseSignatures |
spaSim | Yuzhou Feng | Spatial point data simulator for tissue images |
SpatialCPie | Joseph Bergenstraahle | Cluster analysis of Spatial Transcriptomics data |
spatialDE | Gabriele Sales | R wrapper for SpatialDE |
SpatialDecon | Maddy Griswold | Deconvolution of mixed cells from spatial and/or bulk gene expression data |
SpatialExperiment | Dario Righelli | S4 Class for Spatially Resolved -omics Data |
SpatialFeatureExperiment | Lambda Moses | Integrating SpatialExperiment with Simple Features in sf |
spatialHeatmap | Jianhai Zhang | spatialHeatmap |
SpatialOmicsOverlay | Maddy Griswold | Spatial Overlay for Omic Data from Nanostring GeoMx Data |
spatzie | Jennifer Hammelman | Identification of enriched motif pairs from chromatin interaction data |
speckle | Belinda Phipson | Statistical methods for analysing single cell RNA-seq data |
specL | Christian Panse | specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics |
SpeCond | Florence Cavalli | Condition specific detection from expression data |
Spectra | RforMassSpectrometry Package Maintainer | Spectra Infrastructure for Mass Spectrometry Data |
SpectralTAD | Mikhail Dozmorov | SpectralTAD: Hierarchical TAD detection using spectral clustering |
SpectraQL | Johannes Rainer | MassQL support for Spectra |
SPEM | Xinyi YANG | S-system parameter estimation method |
SPIA | Adi Laurentiu Tarca | Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations |
SPIAT | Yuzhou Feng | Spatial Image Analysis of Tissues |
spicyR | Ellis Patrick | Spatial analysis of in situ cytometry data |
spikeLI | Enrico Carlon | Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool |
spiky | Tim Triche | Spike-in calibration for cell-free MeDIP |
spillR | Marco Guazzini | Spillover Compensation in Mass Cytometry Data |
spkTools | Matthew N McCall | Methods for Spike-in Arrays |
splatter | Luke Zappia | Simple Simulation of Single-cell RNA Sequencing Data |
SpliceWiz | Alex Chit Hei Wong | interactive analysis and visualization of alternative splicing in R |
SplicingFactory | Endre Sebestyen | Splicing Diversity Analysis for Transcriptome Data |
SplicingGraphs | H. Pagès | Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them |
splineTimeR | Herbert Braselmann, Martin Selmansberger | Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction |
SPLINTER | Diana Low | Splice Interpreter of Transcripts |
splots | Wolfgang Huber | Visualization of high-throughput assays in microtitre plate or slide format |
SPONGE | Markus List | Sparse Partial Correlations On Gene Expression |
spoon | Kinnary Shah | Address the Mean-variance Relationship in Spatial Transcriptomics Data |
SpotClean | Zijian Ni | SpotClean adjusts for spot swapping in spatial transcriptomics data |
SPOTlight | Marc Elosua-Bayes | `SPOTlight`: Spatial Transcriptomics Deconvolution |
SpotSweeper | Michael Totty | Spatially-aware quality control for spatial transcriptomics |
spqn | Yi Wang | Spatial quantile normalization |
SPsimSeq | Joris Meys | Semi-parametric simulation tool for bulk and single-cell RNA sequencing data |
SQLDataFrame | Qian Liu | Representation of SQL tables in DataFrame metaphor |
squallms | William Kumler | Speedy quality assurance via lasso labeling for LC-MS data |
sRACIPE | Vivek Kohar | Systems biology tool to simulate gene regulatory circuits |
SRAdb | Jack Zhu | A compilation of metadata from NCBI SRA and tools |
srnadiff | Zytnicki Matthias | Finding differentially expressed unannotated genomic regions from RNA-seq data |
sscu | Yu Sun | Strength of Selected Codon Usage |
sSeq | Danni Yu | Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size |
ssize | Gregory R. Warnes | Estimate Microarray Sample Size |
sSNAPPY | Wenjun Liu | Single Sample directioNAl Pathway Perturbation analYsis |
ssPATHS | Natalie R. Davidson | ssPATHS: Single Sample PATHway Score |
ssrch | VJ Carey | a simple search engine |
ssviz | Diana Low | A small RNA-seq visualizer and analysis toolkit |
StabMap | Shila Ghazanfar | Stabilised mosaic single cell data integration using unshared features |
stageR | Koen Van den Berge | stageR: stage-wise analysis of high throughput gene expression data in R |
standR | Ning Liu | Spatial transcriptome analyses of Nanostring's DSP data in R |
staRank | Juliane Siebourg | Stability Ranking |
STATegRa | David Gomez-Cabrero, Núria Planell | Classes and methods for multi-omics data integration |
Statial | Farhan Ameen | A package to identify changes in cell state relative to spatial associations |
statTarget | Hemi Luan | Statistical Analysis of Molecular Profiles |
STdeconvolve | Brendan Miller | Reference-free Cell-Type Deconvolution of Multi-Cellular Spatially Resolved Transcriptomics Data |
stepNorm | Yuanyuan Xiao | Stepwise normalization functions for cDNA microarrays |
stJoincount | Jiarong Song | stJoincount - Join count statistic for quantifying spatial correlation between clusters |
strandCheckR | Thu-Hien To | Calculate strandness information of a bam file |
Streamer | Martin Morgan | Enabling stream processing of large files |
STRINGdb | Damian Szklarczyk | STRINGdb - Protein-Protein Interaction Networks and Functional Enrichment Analysis |
struct | Gavin Rhys Lloyd | Statistics in R Using Class-based Templates |
Structstrings | Felix G.M. Ernst | Implementation of the dot bracket annotations with Biostrings |
structToolbox | Gavin Rhys Lloyd | Data processing & analysis tools for Metabolomics and other omics |
StructuralVariantAnnotation | Daniel Cameron | Variant annotations for structural variants |
SubCellBarCode | Taner Arslan | SubCellBarCode: Integrated workflow for robust mapping and visualizing whole human spatial proteome |
subSeq | Andrew J. Bass, John D. Storey | Subsampling of high-throughput sequencing count data |
SUITOR | Bill Wheeler | Selecting the number of mutational signatures through cross-validation |
SummarizedBenchmark | Patrick Kimes | Classes and methods for performing benchmark comparisons |
SummarizedExperiment | Hervé Pagès | SummarizedExperiment container |
Summix | Audrey Hendricks | Summix2: A suite of methods to estimate, adjust, and leverage substructure in genetic summary data |
supersigs | Albert Kuo | Supervised mutational signatures |
supraHex | Hai Fang | supraHex: a supra-hexagonal map for analysing tabular omics data |
surfaltr | Pooja Gangras | Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr |
SurfR | Aurora Maurizio | Surface Protein Prediction and Identification |
survClust | Arshi Arora | Identification Of Clinically Relevant Genomic Subtypes Using Outcome Weighted Learning |
survcomp | Benjamin Haibe-Kains | Performance Assessment and Comparison for Survival Analysis |
survtype | Dongmin Jung | Subtype Identification with Survival Data |
sva | Jeffrey T. Leek, John D. Storey, W. Evan Johnson | Surrogate Variable Analysis |
svaNUMT | Ruining Dong | NUMT detection from structural variant calls |
svaRetro | Ruining Dong | Retrotransposed transcript detection from structural variants |
SVMDO | Mustafa Erhan Ozer | Identification of Tumor-Discriminating mRNA Signatures via Support Vector Machines Supported by Disease Ontology |
SWATH2stats | Peter Blattmann | Transform and Filter SWATH Data for Statistical Packages |
SwathXtend | Jemma Wu | SWATH extended library generation and statistical data analysis |
swfdr | Simina M. Boca, Jeffrey T. Leek | Estimation of the science-wise false discovery rate and the false discovery rate conditional on covariates |
switchBox | Bahman Afsari, Luigi Marchionni, Wikum Dinalankara | Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair (KTSP) algorithm |
switchde | Kieran Campbell | Switch-like differential expression across single-cell trajectories |
synapsis | Lucy McNeill | An R package to automate the analysis of double-strand break repair during meiosis |
synapter | Laurent Gatto Sebastian Gibb | Label-free data analysis pipeline for optimal identification and quantitation |
synergyfinder | Shuyu Zheng | Calculate and Visualize Synergy Scores for Drug Combinations |
SynExtend | Nicholas Cooley | Tools for Working With Synteny Objects |
synlet | Chunxuan Shao | Hits Selection for Synthetic Lethal RNAi Screen Data |
SynMut | Haogao Gu | SynMut: Designing Synonymously Mutated Sequences with Different Genomic Signatures |
syntenet | Fabrício Almeida-Silva | Inference And Analysis Of Synteny Networks |
systemPipeR | Thomas Girke | systemPipeR: Workflow Environment for Data Analysis and Report Generation |
systemPipeShiny | Le Zhang | systemPipeShiny: An Interactive Framework for Workflow Management and Visualization |
systemPipeTools | Daniela Cassol | Tools for data visualization |
tadar | Lachlan Baer | Transcriptome Analysis of Differential Allelic Representation |
TADCompare | Mikhail Dozmorov | TADCompare: Identification and characterization of differential TADs |
tanggle | Klaus Schliep | Visualization of Phylogenetic Networks |
TAPseq | Andreas R. Gschwind | Targeted scRNA-seq primer design for TAP-seq |
target | Mahmoud Ahmed | Predict Combined Function of Transcription Factors |
TargetDecoy | Elke Debrie | Diagnostic Plots to Evaluate the Target Decoy Approach |
TargetScore | Yue Li | TargetScore: Infer microRNA targets using microRNA-overexpression data and sequence information |
TargetSearch | Alvaro Cuadros-Inostroza | A package for the analysis of GC-MS metabolite profiling data |
TBSignatureProfiler | Aubrey R. Odom | Profile RNA-Seq Data Using TB Pathway Signatures |
TCC | Jianqiang Sun, Tomoaki Nishiyama | TCC: Differential expression analysis for tag count data with robust normalization strategies |
TCGAbiolinks | Tiago Chedraoui Silva, Antonio Colaprico | TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data |
TCGAutils | Marcel Ramos | TCGA utility functions for data management |
TCseq | Mengjun Wu | Time course sequencing data analysis |
TDbasedUFE | Y-h. Taguchi | Tensor Decomposition Based Unsupervised Feature Extraction |
TDbasedUFEadv | Y-h. Taguchi | Advanced package of tensor decomposition based unsupervised feature extraction |
TEKRABber | Yao-Chung Chen | An R package estimates the correlations of orthologs and transposable elements between two species |
TENxIO | Marcel Ramos | Import methods for 10X Genomics files |
tenXplore | VJ Carey | ontological exploration of scRNA-seq of 1.3 million mouse neurons from 10x genomics |
TEQC | Sarah Bonnin | Quality control for target capture experiments |
ternarynet | McCall N. Matthew | Ternary Network Estimation |
terraTCGAdata | Marcel Ramos | OpenAccess TCGA Data on Terra as MultiAssayExperiment |
TFARM | Liuba Nausicaa Martino | Transcription Factors Association Rules Miner |
TFBSTools | Ge Tan | Software Package for Transcription Factor Binding Site (TFBS) Analysis |
TFEA.ChIP | Laura Puente Santamaría | Analyze Transcription Factor Enrichment |
TFHAZ | Gaia Ceddia | Transcription Factor High Accumulation Zones |
TFutils | Vincent Carey | TFutils |
tidybulk | Stefano Mangiola | Brings transcriptomics to the tidyverse |
tidyCoverage | Jacques Serizay | Extract and aggregate genomic coverage over features of interest |
tidyFlowCore | Timothy Keyes | tidyFlowCore: Bringing flowCore to the tidyverse |
tidyomics | Stefano Mangiola | Easily install and load the tidyomics ecosystem |
tidysbml | Veronica Paparozzi | Extract SBML's data into dataframes |
tidySingleCellExperiment | Stefano Mangiola | Brings SingleCellExperiment to the Tidyverse |
tidySpatialExperiment | William Hutchison | SpatialExperiment with tidy principles |
tidySummarizedExperiment | Stefano Mangiola | Brings SummarizedExperiment to the Tidyverse |
tidytof | Timothy Keyes | Analyze High-dimensional Cytometry Data Using Tidy Data Principles |
tigre | Antti Honkela | Transcription factor Inference through Gaussian process Reconstruction of Expression |
TileDBArray | Aaron Lun | Using TileDB as a DelayedArray Backend |
tilingArray | Zhenyu Xu | Transcript mapping with high-density oligonucleotide tiling arrays |
timecourse | Yu Chuan Tai | Statistical Analysis for Developmental Microarray Time Course Data |
timeOmics | Antoine Bodein | Time-Course Multi-Omics data integration |
timescape | Maia Smith | Patient Clonal Timescapes |
TIN | Bjarne Johannessen | Transcriptome instability analysis |
TissueEnrich | Ashish Jain | Tissue-specific gene enrichment analysis |
TitanCNA | Gavin Ha | Subclonal copy number and LOH prediction from whole genome sequencing of tumours |
tkWidgets | J. Zhang | R based tk widgets |
tLOH | Michelle Webb | Assessment of evidence for LOH in spatial transcriptomics pre-processed data using Bayes factor calculations |
TMixClust | Monica Golumbeanu | Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines |
TnT | Jialin Ma | Interactive Visualization for Genomic Features |
TOAST | Ziyi Li | Tools for the analysis of heterogeneous tissues |
tomoda | Wendao Liu | Tomo-seq data analysis |
tomoseqr | Ryosuke Matsuzawa | R Package for Analyzing Tomo-seq Data |
TOP | Harry Robertson | TOP Constructs Transferable Model Across Gene Expression Platforms |
topconfects | Paul Harrison | Top Confident Effect Sizes |
topdownr | Sebastian Gibb | Investigation of Fragmentation Conditions in Top-Down Proteomics |
topGO | Adrian Alexa | Enrichment Analysis for Gene Ontology |
ToxicoGx | Benjamin Haibe-Kains | Analysis of Large-Scale Toxico-Genomic Data |
TPP | Dorothee Childs | Analyze thermal proteome profiling (TPP) experiments |
TPP2D | Nils Kurzawa | Detection of ligand-protein interactions from 2D thermal profiles (DLPTP) |
tpSVG | Boyi Guo | Thin plate models to detect spatially variable genes |
tracktables | Tom Carroll | Build IGV tracks and HTML reports |
trackViewer | Jianhong Ou | A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data |
tradeSeq | Hector Roux de Bezieux | trajectory-based differential expression analysis for sequencing data |
TrajectoryGeometry | Michael Shapiro | This Package Discovers Directionality in Time and Pseudo-times Series of Gene Expression Patterns |
TrajectoryUtils | Aaron Lun | Single-Cell Trajectory Analysis Utilities |
transcriptogramer | Diego Morais | Transcriptional analysis based on transcriptograms |
transcriptR | Armen R. Karapetyan | An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification |
transformGamPoi | Constantin Ahlmann-Eltze | Variance Stabilizing Transformation for Gamma-Poisson Models |
transite | Konstantin Krismer | RNA-binding protein motif analysis |
tRanslatome | Toma Tebaldi, Erik Dassi | Comparison between multiple levels of gene expression |
transmogR | Stevie Pederson | Modify a set of reference sequences using a set of variants |
transomics2cytoscape | Kozo Nishida | A tool set for 3D Trans-Omic network visualization with Cytoscape |
TransView | Julius Muller | Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets |
traseR | li chen | GWAS trait-associated SNP enrichment analyses in genomic intervals |
traviz | Koen Van den Berge | Trajectory functions for visualization and interpretation. |
TreeAndLeaf | Milena A. Cardoso | Displaying binary trees with focus on dendrogram leaves |
treeclimbR | Charlotte Soneson | An algorithm to find optimal signal levels in a tree |
treeio | Guangchuang Yu | Base Classes and Functions for Phylogenetic Tree Input and Output |
treekoR | Adam Chan | Cytometry Cluster Hierarchy and Cellular-to-phenotype Associations |
TreeSummarizedExperiment | Ruizhu Huang | TreeSummarizedExperiment: a S4 Class for Data with Tree Structures |
TREG | Louise Huuki-Myers | Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data |
Trendy | Rhonda Bacher | Breakpoint analysis of time-course expression data |
TRESS | Zhenxing Guo | Toolbox for mRNA epigenetics sequencing analysis |
tricycle | Shijie Zheng | tricycle: Transferable Representation and Inference of cell cycle |
trigger | John D. Storey | Transcriptional Regulatory Inference from Genetics of Gene ExpRession |
trio | Holger Schwender | Testing of SNPs and SNP Interactions in Case-Parent Trio Studies |
triplex | Jiri Hon | Search and visualize intramolecular triplex-forming sequences in DNA |
tripr | Nikolaos Pechlivanis | T-cell Receptor/Immunoglobulin Profiler (TRIP) |
tRNA | Felix GM Ernst | Analyzing tRNA sequences and structures |
tRNAdbImport | Felix G.M. Ernst | Importing from tRNAdb and mitotRNAdb as GRanges objects |
tRNAscanImport | Felix G.M. Ernst | Importing a tRNAscan-SE result file as GRanges object |
TRONCO | Luca De Sano | TRONCO, an R package for TRanslational ONCOlogy |
TSAR | Xinlin Gao | Thermal Shift Analysis in R |
TSCAN | Zhicheng Ji | Tools for Single-Cell Analysis |
ttgsea | Dongmin Jung | Tokenizing Text of Gene Set Enrichment Analysis |
TTMap | Rachel Jeitziner | Two-Tier Mapper: a clustering tool based on topological data analysis |
TurboNorm | Maarten van Iterson | A fast scatterplot smoother suitable for microarray normalization |
TVTB | Kevin Rue-Albrecht | TVTB: The VCF Tool Box |
tweeDEseq | Dolors Pelegri-Siso | RNA-seq data analysis using the Poisson-Tweedie family of distributions |
twilight | Stefanie Scheid | Estimation of local false discovery rate |
twoddpcr | Anthony Chiu | Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting molecules |
txcutr | Mervin Fansler | Transcriptome CUTteR |
txdbmaker | H. Pagès | Tools for making TxDb objects from genomic annotations |
tximeta | Michael Love | Transcript Quantification Import with Automatic Metadata |
tximport | Michael Love | Import and summarize transcript-level estimates for transcript- and gene-level analysis |
TypeInfo | Duncan Temple Lang | Optional Type Specification Prototype |
UCell | Massimo Andreatta | Rank-based signature enrichment analysis for single-cell data |
UCSC.utils | Hervé Pagès | Low-level utilities to retrieve data from the UCSC Genome Browser |
Ularcirc | David Humphreys | Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis) |
UMI4Cats | Mireia Ramos-Rodriguez | UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data |
uncoverappLib | Emanuela Iovino | Interactive graphical application for clinical assessment of sequence coverage at the base-pair level |
UNDO | Niya Wang | Unsupervised Deconvolution of Tumor-Stromal Mixed Expressions |
unifiedWMWqPCR | Joris Meys | Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data |
UniProt.ws | Marcel Ramos | R Interface to UniProt Web Services |
Uniquorn | 'Raik Otto' | Identification of cancer cell lines based on their weighted mutational/ variational fingerprint |
universalmotif | Benjamin Jean-Marie Tremblay | Import, Modify, and Export Motifs with R |
updateObject | Hervé Pagès | Find/fix old serialized S4 instances |
UPDhmm | Marta Sevilla | Detecting Uniparental Disomy through NGS trio data |
uSORT | Hao Chen | uSORT: A self-refining ordering pipeline for gene selection |
VAExprs | Dongmin Jung | Generating Samples of Gene Expression Data with Variational Autoencoders |
VanillaICE | Robert Scharpf | A Hidden Markov Model for high throughput genotyping arrays |
VarCon | Johannes Ptok | VarCon: an R package for retrieving neighboring nucleotides of an SNV |
variancePartition | Gabriel E. Hoffman | Quantify and interpret drivers of variation in multilevel gene expression experiments |
VariantAnnotation | Bioconductor Package Maintainer | Annotation of Genetic Variants |
VariantExperiment | Qian Liu | A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend |
VariantFiltering | Robert Castelo | Filtering of coding and non-coding genetic variants |
VariantTools | Michael Lawrence | Tools for Exploratory Analysis of Variant Calls |
VaSP | Huihui Yu | Quantification and Visualization of Variations of Splicing in Population |
vbmp | Nicola Lama | Variational Bayesian Multinomial Probit Regression |
VCFArray | Qian Liu | Representing on-disk / remote VCF files as array-like objects |
VDJdive | Kelly Street | Analysis Tools for 10X V(D)J Data |
VegaMC | Sandro Morganella | VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer |
velociraptor | Kevin Rue-Albrecht | Toolkit for Single-Cell Velocity |
veloviz | Lyla Atta | VeloViz: RNA-velocity informed 2D embeddings for visualizing cell state trajectories |
VennDetail | Kai Guo | A package for visualization and extract details |
VERSO | Davide Maspero | Viral Evolution ReconStructiOn (VERSO) |
vidger | Brandon Monier | Create rapid visualizations of RNAseq data in R |
viper | Mariano J Alvarez | Virtual Inference of Protein-activity by Enriched Regulon analysis |
ViSEAGO | Aurelien Brionne | ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity |
VisiumIO | Marcel Ramos | Import Visium data from the 10X Space Ranger pipeline |
vissE | Dharmesh D. Bhuva | Visualising Set Enrichment Analysis Results |
Voyager | Lambda Moses | From geospatial to spatial omics |
VplotR | Jacques Serizay | Set of tools to make V-plots and compute footprint profiles |
vsclust | Veit Schwaemmle | Feature-based variance-sensitive quantitative clustering |
vsn | Wolfgang Huber | Variance stabilization and calibration for microarray data |
vtpnet | VJ Carey | variant-transcription factor-phenotype networks |
vulcan | Federico M. Giorgi | VirtUaL ChIP-Seq data Analysis using Networks |
waddR | Julian Flesch | Statistical tests for detecting differential distributions based on the 2-Wasserstein distance |
wateRmelon | Leo C Schalkwyk | Illumina DNA methylation array normalization and metrics |
wavClusteR | Federico Comoglio | Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data |
weaver | Seth Falcon | Tools and extensions for processing Sweave documents |
webbioc | Colin A. Smith | Bioconductor Web Interface |
weitrix | Paul Harrison | Tools for matrices with precision weights, test and explore weighted or sparse data |
widgetTools | Jianhua Zhang | Creates an interactive tcltk widget |
wiggleplotr | Kaur Alasoo | Make read coverage plots from BigWig files |
wpm | Helene Borges | Well Plate Maker |
wppi | Ana Galhoz | Weighting protein-protein interactions |
Wrench | Hector Corrada Bravo | Wrench normalization for sparse count data |
xcms | Steffen Neumann | LC-MS and GC-MS Data Analysis |
xcore | Maciej Migdał | xcore expression regulators inference |
XDE | Robert Scharpf | XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression |
xenLite | Vincent Carey | Simple classes and methods for managing Xenium datasets |
Xeva | Benjamin Haibe-Kains | Analysis of patient-derived xenograft (PDX) data |
XINA | Lang Ho Lee and Sasha A. Singh | Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis |
xmapbridge | Chris Wirth | Export plotting files to the xmapBridge for visualisation in X:Map |
XNAString | Marianna Plucinska | Efficient Manipulation of Modified Oligonucleotide Sequences |
XVector | Hervé Pagès | Foundation of external vector representation and manipulation in Bioconductor |
yamss | Leslie Myint | Tools for high-throughput metabolomics |
YAPSA | Zuguang Gu | Yet Another Package for Signature Analysis |
yarn | Joseph N Paulson | YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization |
zellkonverter | Luke Zappia | Conversion Between scRNA-seq Objects |
zenith | Gabriel Hoffman | Gene set analysis following differential expression using linear (mixed) modeling with dream |
zFPKM | Ron Ammar | A suite of functions to facilitate zFPKM transformations |
zinbwave | Davide Risso | Zero-Inflated Negative Binomial Model for RNA-Seq Data |
zitools | Carlotta Meyring | Analysis of zero-inflated count data |
zlibbioc | Bioconductor Package Maintainer | An R packaged zlib-1.2.5 |
ZygosityPredictor | Marco Rheinnecker | Package for prediction of zygosity for variants/genes in NGS data |