| Package | Maintainer | Title |
|---|---|---|
| ABarray | Yongming Andrew Sun | Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Micorarray (AB1700) gene expression data. |
| aCGH | Jane Fridlyand | Classes and functions for Array Comparative Genomic Hybridization data. |
| ACME | Sean Davis | Algorithms for Calculating Microarray Enrichment (ACME) |
| adSplit | Claudio Lottaz | Annotation-Driven Clustering |
| affxparser | Kasper Daniel Hansen | Affymetrix File Parsing SDK |
| affy | Rafael A. Irizarry | Methods for Affymetrix Oligonucleotide Arrays |
| affycomp | Rafael A. Irizarry | Graphics Toolbox for Assessment of Affymetrix Expression Measures |
| affycoretools | James W. MacDonald | Functions useful for those doing repetitive analyses with Affymetrix GeneChips. |
| AffyExpress | Xuejun Arthur Li | Affymetrix Quality Assessment and Analysis Tool |
| affyio | Benjamin Milo Bolstad | Tools for parsing Affymetrix data files |
| affylmGUI | Keith Satterley | GUI for affy analysis using limma package |
| affypdnn | Laurent Gautier | Probe Dependent Nearest Neighbours (PDNN) for the affy package |
| affyPLM | Ben Bolstad | Methods for fitting probe-level models |
| affyQCReport | Craig Parman | QC Report Generation for affyBatch objects |
| altcdfenvs | Laurent Gautier | alternative cdfenvs |
| annaffy | Colin A. Smith | Annotation tools for Affymetrix biological metadata |
| AnnBuilder | J. Zhang | Bioconductor annotation data package builder |
| annotate | Biocore Team c/o BioC user list | Annotation for microarrays |
| AnnotationDbi | Biocore Team c/o BioC user list | Annotation Database Interface |
| annotationTools | Alexandre Kuhn | Annotate microarrays and perform cross-species gene expression analyses using flat file databases. |
| apComplex | Denise Scholtens | Estimate protein complex membership using AP-MS protein data |
| aroma.light | Henrik Bengtsson | Light-weight methods for normalization and visualization of microarray data using only basic R data types |
| arrayMagic | Andreas Buness | two-colour cDNA array quality control and preprocessing |
| arrayQuality | Agnes Paquet | Assessing array quality on spotted arrays |
| arrayQualityMetrics | Audrey Kauffmann | Quality metrics on ExpressionSets |
| beadarray | Mark Dunning | Quality control and low-level analysis of BeadArrays |
| beadarraySNP | Jan Oosting | Normalization and reporting of Illumina SNP bead arrays |
| BeadExplorer | Gareth Elvidge | QC, normalisation, annotation and exploration of Illumina BeadChip data |
| bgafun | Iain Wallace | BGAfun A method to identify specifity determining residues in protein families |
| bgx | Ernest Turro | Bayesian Gene eXpression |
| Biobase | Biocore Team c/o BioC user list | Biobase: Base functions for Bioconductor |
| biocGraph | Li Long | Graph examples and use cases in Bioinformatics |
| biocViews | Biocore Team c/o BioC user list | Categorized views of R package repositories |
| bioDist | Biocore Team c/o BioC user list | Different distance measures |
| biomaRt | Steffen Durinck | Interface to BioMart databases (e.g. Ensembl, Wormbase, Gramene and Uniprot) |
| BioMVCClass | Elizabeth Whalen | Model-View-Controller (MVC) Classes That Use Biobase |
| Biostrings | H. Pages | String objects representing biological sequences, and matching algorithms |
| bridge | Raphael Gottardo | Bayesian Robust Inference for Differential Gene Expression |
| BSgenome | H. Pages | Infrastructure for Biostrings-based genome data packages |
| BufferedMatrix | Benjamin Milo Bolstad | A matrix data storage object held in temporary files |
| BufferedMatrixMethods | B. M. Bolstad | Microarray Data related methods that utlize BufferedMatrix objects |
| CALIB | Hui Zhao | Calibration model for estimating absolute expression levels from microarray data |
| Category | Robert Gentleman | Category Analysis |
| cellHTS | Ligia Bras | Analysis of cell-based screens |
| cellHTS2 | Ligia Bras | Analysis of cell-based screens - revised version of cellHTS |
| CGHcall | Sjoerd Vosse | Calling aberrations for array CGH tumor profiles. |
| cghMCR | J. Zhang | Find chromosome regions showing common gains/losses |
| ChromoViz | Jihoon Kim | Multimodal visualization of gene expression data |
| clusterStab | James W. MacDonald | Compute cluster stability scores for microarray data |
| CoCiteStats | R. Gentleman | Different test statistics based on co-citation. |
| codelink | Diego Diez | Manipulation of Codelink Bioarrays data. |
| convert | Yee Hwa (Jean) Yang | Convert Microarray Data Objects |
| copa | James W. MacDonald | Functions to perform cancer outlier profile analysis. |
| CORREP | Dongxiao Zhu | Multivariate Correlation Estimator and Statistical Inference Procedures. |
| cosmo | Oliver Bembom | Supervised detection of conserved motifs in DNA sequences |
| cosmoGUI | Oliver Bembom | GUI for constructing constraint sets used by the cosmo package |
| ctc | Antoine Lucas | Cluster and Tree Conversion. |
| daMA | Jobst Landgrebe | Efficient design and analysis of factorial two-colour microarray data |
| DEDS | Yuanyuan Xiao | Differential Expression via Distance Summary for Microarray Data |
| diffGeneAnalysis | Choudary Jagarlamudi | Performs differential gene expression Analysis |
| DNAcopy | Venkatraman E. Seshan | DNA copy number data analysis |
| DynDoc | Biocore Team c/o BioC user list | Dynamic document tools |
| EBarrays | Ming Yuan | Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification |
| EBImage | Oleg Sklyar | Image processing and image analysis toolkit for R |
| ecolitk | Laurent | Meta-data and tools for E. coli |
| edd | Vince Carey | expression density diagnostics |
| exonmap | Crispin Miller | High level analysis of Affymetrix exon array data |
| explorase | Michael Lawrence | GUI for exploratory data analysis of systems biology data |
| factDesign | Denise Scholtens | Factorial designed microarray experiment analysis |
| fbat | Weiliang Qiu | Family Based Association Tests for genetic data. |
| fdrame | Effi Kenigsberg | FDR adjustments of Microarray Experiments (FDR-AME) |
| flowCore | Nolwenn Le Meur | flowCore: Basic structures for flow cytometry data |
| flowUtils | Florian Hahne | Utilities for flow cytometry |
| flowViz | Florian Hahne | Visualization for flow cytometry |
| gaggle | Paul Shannon | Broadcast data between R and Java bioinformatics programs |
| gcrma | Z. Wu | Background Adjustment Using Sequence Information |
| genArise | IFC Development Team | Microarray Analysis tool |
| genefilter | Biocore Team c/o BioC user list | genefilter: methods for filtering genes from microarray experiments |
| GeneMeta | Biocore Team c/o BioC user list | MetaAnalysis for High Throughput Experiments |
| geneplotter | Biocore Team c/o BioC user list | Grapics related functions for Bioconductor |
| GeneR | Y. d'Aubenton-Carafa | R for genes and sequences analysis |
| geneRecommender | Greg Hather | A gene recommender algorithm to identify genes coexpressed with a query set of genes |
| GeneSpring | Thon de Boer | GeneSpring R Integration Functions |
| GeneticsBase | Gregory Warnes | Classes and functions for handling genetic data |
| GeneticsDesign | Weiliang Qiu | Functions for designing genetics studies |
| GeneTraffic | Daniel Iordan | GeneTraffic R Integration Functions |
| GeneTS | Korbinian Strimmer | Microarray Time Series and Network Analysis |
| GEOquery | Sean Davis | Get data from NCBI Gene Expression Omnibus (GEO) |
| GGtools | Vince Carey | software and data for genetical genomics (c) 2006 VJ Carey |
| GLAD | Philippe Hupe | Gain and Loss Analysis of DNA |
| GlobalAncova | R. Meister | Calculates a global test for differential gene expression between groups |
| globaltest | Jelle Goeman | Testing Association of Groups of Genes with a Clinical Variable |
| GOstats | Robert Gentleman | Tools for manipulating GO and microarrays. |
| goTools | Agnes Paquet | Functions for Gene Ontology database |
| gpls | Biocore Team c/o BioC user list | Classification using generalized partial least squares |
| graph | Robert Gentleman | graph: A package to handle graph data structures |
| GraphAT | Thomas LaFramboise | Graph Theoretic Association Tests |
| GSEABase | Biocore Team c/o BioC user list | Gene set enrichment data structures and methods |
| Harshlight | Maurizio Pellegrino | A "corrective make-up" program for microarray chips |
| Heatplus | Alexander Ploner | A heat map displaying covariates and coloring clusters |
| HEM | HyungJun Cho | Heterogeneous error model for identification of differentially expressed genes under multiple conditions |
| hexbin | Nicholas Lewin-Koh | Hexagonal Binning Routines |
| hopach | Katherine S. Pollard | Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) |
| hypergraph | Robert Gentleman | A package providing hypergraph data structures |
| Icens | Biocore Team c/o BioC user list | NPMLE for Censored and Truncated Data |
| idiogram | Karl J. Dykema | idiogram |
| impute | Balasubramanian Narasimhan | impute: Imputation for microarray data |
| iSNetwork | Elizabeth Whalen | Interactive Network Plots |
| iSPlot | Elizabeth Whalen | Linking Plots |
| keggorth | VJ Carey | graph support for KO, KEGG Orthology |
| KEGGSOAP | Robert Gentleman | Client-side SOAP access KEGG |
| lapmix | Yann Ruffieux | Laplace Mixture Model in Microarray Experiments |
| LBE | Cyril Dalmasso | Estimation of the false discovery rate. |
| limma | Gordon Smyth | Linear Models for Microarray Data |
| limmaGUI | Keith Satterley | GUI for limma package |
| LMGene | John Tillinghast | LMGene Software for Date Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays |
| logicFS | Holger Schwender | Identification of SNP Interactions |
| LPE | Nitin Jain | Methods for analyzing microarray data using Local Pooled Error (LPE) method |
| lumi | Pan Du | BeadArray Specific Methods for Illumina Microarrays |
| maanova | Hyuna Yang | Tools for analyzing Micro Array experiments |
| macat | Joern Toedling | MicroArray Chromosome Analysis Tool |
| maCorrPlot | Alexander Ploner | Visualize artificial correlation in microarray data |
| maDB | Johannes Rainer | Microarray database and utility functions for microarray data analysis. |
| made4 | Aedin Culhane | Multivariate analysis of microarray data using ADE4 |
| maigesPack | Gustavo H. Esteves | Functions to handle cDNA microarray data, including several methods of data analysis |
| makecdfenv | James W. MacDonald | CDF Environment Maker |
| makePlatformDesign | Benilton Carvalho | Platform Design Package |
| MANOR | Pierre Neuvial | CGH Micro-Array NORmalization |
| MantelCorr | Brian Steinmeyer | Compute Mantel Cluster Correlations |
| marray | Yee Hwa (Jean) Yang | Exploratory analysis for two-color spotted microarray data |
| maSigPro | Ana Conesa | Significant Gene Expression Profile Differeneces in Time Course Microarray Data |
| MassSpecWavelet | Pan Du | Mass spectrum processing by wavelet-based algorithms |
| matchprobes | Biocore Team c/o BioC user list | Tools for sequence matching of probes on arrays |
| MCRestimate | Markus Ruschhaupt | Misclassification error estimation with cross-validation |
| MeasurementError.cor | Beiying Ding | Measurement Error model estimate for correlation coefficient |
| MergeMaid | Xiaogang Zhong | Merge Maid |
| metaArray | Hyungwon Choi | Integration of Microarray Data for Meta-analysis |
| Mfuzz | Matthias Futschik | Soft clustering of time series gene expression data |
| MiPP | Sukwoo Kim | Misclassification Penalized Posterior Classification |
| MLInterfaces | V. Carey | Uniform interfaces to R machine learning procedures for data in Bioconductor containers |
| multtest | Katherine S. Pollard | Resampling-based multiple hypothesis testing |
| MVCClass | Elizabeth Whalen | Model-View-Controller (MVC) Classes |
| nem | Florian Markowetz | Nested Effects Models to reconstruct phenotypic hierarchies |
| nnNorm | Adi Laurentiu Tarca | Spatial and intensity based normalization of cDNA microarray data based on robust neural nets |
| OCplus | Alexander Ploner | Operating characteristics plus sample size and local fdr for microarray experiments |
| oligo | Benilton Carvalho | Oligonucleotide Arrays |
| oligoClasses | Benilton Carvalho | Classes for high-throughput SNP arrays |
| OLIN | Matthias Futschik | Optimized local intensity-dependent normalisation of two-color microarrays |
| OLINgui | Matthias Futschik | Graphical user interface for OLIN |
| oneChannelGUI | Raffaele A Calogero | This package extends the capabilities of affylmGUI graphical interface. |
| ontoTools | Vince Carey | graphs and sparse matrices for working with ontologies; formal objects for nomenclatures with provenance management |
| OrderedList | Claudio Lottaz | Similarities of Ordered Gene Lists |
| OutlierD | Sukwoo Kim | Outlier detection using quantile regression on the M-A scatterplots of high-throughput data |
| pamr | Rob Tibshirani | Pam: prediction analysis for microarrays |
| panp | Peter Warren | Presence-Absence Calls from Negative Strand Matching Probesets |
| pathRender | Li Long | Render molecular pathways |
| pcaMethods | Wolfram Stacklies | A collection of PCA methods. |
| pcot2 | Sarah Song | Principal Coordinates and Hotelling's T-Square method |
| pdInfoBuilder | Vince Carey | Platform Design Information Package Builder |
| pdmclass | James W. MacDonald | Classification of Microarray Samples using Penalized Discriminant Methods |
| PGSEA | Karl Dykema | Parametric Gene Set Enrichment Analysis |
| pgUtils | Johannes Rainer | Utility functions for PostgreSQL databases |
| pickgene | Brian S. Yandell | Adaptive Gene Picking for Microarray Expression Data Analysis |
| pkgDepTools | Seth Falcon | Package Dependency Tools |
| plgem | Mattia Pelizzola | Power Law Global Error Model |
| plier | Crispin Miller | Implements the Affymetrix PLIER algorithm |
| ppiStats | Tony Chiang | Protein-Protein Interaction Statistical Package |
| prada | Florian Hahne | Data analysis for cell-based functional assays |
| preprocessCore | Benjamin Milo Bolstad | A collection of pre-processing functions |
| PROcess | Xiaochun Li | Ciphergen SELDI-TOF Processing |
| puma | Richard Pearson | Propagating Uncertainty in Microarray Analysis |
| quantsmooth | Jan Oosting | Quantile smoothing and genomic visualization of array data |
| qvalue | John D. Storey | Q-value estimation for false discovery rate control |
| rama | Raphael Gottardo | Robust Analysis of MicroArrays |
| RankProd | Fangxin Hong | Rank Product method for identifying differentially expressed genes with application in meta-analysis |
| RbcBook1 | Vince Carey | Support for Springer monograph on Bioconductor |
| RBGL | Li Long | Interface to boost C++ graph lib |
| rbsurv | Sukwoo Kim | Robust likelihood-based survival modeling with microarray data |
| Rdbi | Jianhua Zhang | Generic database methods |
| RdbiPgSQL | Jianhua Zhang | PostgreSQL access |
| reb | Karl J. Dykema | Regional Expression Biases |
| RefPlus | Kai-Ming Chang | A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods. |
| Resourcerer | Jianhua Zhang | Reads annotation data from TIGR Resourcerer or convert the annotation data into Bioconductor data pacakge. |
| rflowcyt | N. LeMeur | Statistical tools and data structures for analytic flow cytometry |
| Rgraphviz | Li Long | Provides plotting capabilities for R graph objects |
| rHVDM | Martino Barenco | Hidden Variable Dynamic Modeling |
| Ringo | J. Toedling | R Investigation of NimbleGen Oligoarrays |
| Rintact | Tony Chiang | Interface to EBI Intact protein interaction data base |
| RLMM | Nusrat Rabbee | A Genotype Calling Algorithm for Affymetrix SNP Arrays |
| RMAGEML | Steffen Durinck | Handling MAGEML documents |
| RMAPPER | VJ Carey | interface to mapper.chip.org |
| ROC | Vince Carey | utilities for ROC, with uarray focus |
| rsbml | Michael Lawrence | R support for SBML, using libsbml |
| RSNPper | VJ Carey | interface to chip.org::SNPper for SNP-related data |
| Ruuid | Biocore Team c/o BioC user list | Ruuid: Provides Universally Unique ID values |
| RWebServices | Biocore Team c/o BioC user list | Expose R functions as web services through Java/Axis/Apache |
| safe | William T. Barry | Significance Analysis of Function and Expression |
| SAGElyzer | Jianhua Zhang | A package that deals with SAGE libraries |
| sagenhaft | Tim Beissbarth | Collection of functions for reading and comparing SAGE libraries |
| SAGx | Per Broberg | Statistical Analysis of the GeneChip |
| SBMLR | Tomas Radivoyevitch | SBML-R Interface and Analysis Tools |
| ScISI | Tony Chiang | In Silico Interactome |
| SemSim | Xiang Guo | Gene Ontology-based Semantic Similarity Measures |
| seqLogo | Oliver Bembom | Sequence logos for DNA sequence alignments |
| siggenes | Holger Schwender | Multiple testing using SAM and Efron's empirical Bayes approaches |
| sigPathway | Weil Lai | Pathway Analysis |
| simpleaffy | Crispin Miller | Very simple high level analysis of Affymetrix data |
| simulatorAPMS | Tony Chiang | Computationally simulates the AP-MS technology. |
| sizepower | Weiliang Qiu | Sample Size and Power Calculation in Micorarray Studies |
| SLqPCR | Matthias Kohl | Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH |
| SMAP | Robin Andersson | A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling |
| snapCGH | John Marioni | Segmentation, normalisation and processing of aCGH data. |
| SNPchip | Robert Scharpf | Classes and Methods for high throughput SNP chip data |
| spikeLI | Enrico Carlon | Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool |
| splicegear | Laurent | splicegear |
| splots | Oleg Sklyar | Visualization routines for high throughput screens |
| spotSegmentation | Chris Fraley | Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots |
| sscore | Richard Kennedy | S-Score Algorithm for Affymetrix Oligonucleotide Microarrays |
| ssize | Gregory R. Warnes | Estimate Microarry Sample Size |
| stepNorm | Yuanyuan Xiao | Stepwise normalization functions for cDNA microarrays |
| tilingArray | W. Huber | Analysis of high-density oligonucleotide tiling arrays |
| timecourse | Yu Chuan Tai | Statistical Analysis for Developmental Microarray Time Course Data |
| tkWidgets | J. Zhang | R based tk widgets |
| topGO | Adrian Alexa | topGO: Enrichment analysis for Gene Ontology |
| twilight | Stefanie Scheid | Estimation of local false discovery rate |
| TypeInfo | Duncan Temple Lang | Optional Type Specification Prototype |
| VanillaICE | Robert Scharpf | Methods for fitting Hidden Markov Models to SNP chip data |
| vbmp | Nicola Lama | Variational Bayesian Multinomial Probit Regression |
| vsn | Wolfgang Huber | Variance stabilization and calibration for microarray data |
| weaver | Seth Falcon | Tools and extensions for processing Sweave documents |
| webbioc | Colin A. Smith | Bioconductor Web Interface |
| widgetInvoke | Jeff Gentry | Evaluation widgets for functions |
| widgetTools | Jianhua Zhang | Creates an interactive tcltk widget |
| xcms | Colin A. Smith | LC/MS and GC/MS Data Analysis |