Bioconductor Task View: Software

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Package Maintainer Title
aCGH Jane Fridlyand Classes and functions for Array Comparative Genomic Hybridization data.
adSplit Claudio Lottaz Annotation-Driven Clustering
affxparser James Bullard 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.
affydata Laurent Affymetrix Data for Demonstration Purpose
affyio Benjamin Milo Bolstad Tools for parsing Affymetrix data files
affylmGUI Keith Satterley GUI for affy analysis using limma package
affypdnn Laurent 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 Annotation for microarrays
apComplex Denise Scholtens Estimate protein complex membership using AP-MS protein data
applera Francesca Cordero applera
arrayMagic Andreas Buness two-colour cDNA array quality control and preprocessing
arrayQuality A. Paquet Assessing array quality on spotted arrays
beadarray Mark Dunning Quality control and low-level analysis of BeadArrays
bim Brian S. Yandell Bayesian Interval Mapping Diagnostics
Biobase Biocore Team Biobase: Base functions for Bioconductor
biocViews Seth Falcon Categorized views of R package repositories
bioDist Biocore Team Different distance measures
biomaRt Steffen Durinck Interface to BioMart databases (e.g. Ensembl)
Biostrings H. Pages String objects representing biological sequences, and matching algorithms
bridge Raphael Gottardo Bayesian Robust Inference for Differential Gene Expression
Category R. Gentleman Category Analysis
cellHTS Wolfgang Huber Analysis of cell-based screens
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 Díez 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.
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 E. S. Venkatraman DNA copy number data analysis
DynDoc Biocore Team Dynamic document tools
EBarrays Deepayan Sarkar Empirical Bayes for Microarrays
EBImage Oleg Sklyar EBImage: R image processing toolkit
ecolitk Laurent Meta-data and tools for E. coli
edd Vince Carey expression density diagnostics
exprExternal Biocore Team Implementation of exprSet using externalVectors
externalVector Biocore Team Vector objects for R with external storage
factDesign Denise Scholtens Factorial designed microarray experiment analysis
fdrame Effi Kenigsberg FDR adjustments of Microarray Experiments (FDR-AME)
gcrma Z. Wu Background Adjustment Using Sequence Information
genArise IFC Development Team Microarray Analysis tool
genefilter Biocore Team genefilter: filter genes
GeneMeta Biocore Team MetaAnalysis for High Throughput Experiments
geneplotter Biocore Team 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
GeneTraffic Daniel Iordan GeneTraffic R Integration Functions
GeneTS Korbinian Strimmer Microarray Time Series and Network Analysis
GenomeBase H. Pages Base functions for genome data package manipulation
GEOquery Sean Davis Get data from NCBI Gene Expression Omnibus (GEO)
gff3Plotter Oleg Sklyar Plotting Data of Experiments on the Genomic Layout
GLAD Philippe Hupé 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
goCluster Gunnar Wrobel Analysis of clustering results in conjunction with annotation data.
GOstats R. Gentleman Tools for manipulating GO and microarrays.
goTools Agnes Paquet Functions for Gene Ontology database
gpls Biocore Team Classification using generalized partial least squares
graph Seth Falcon graph: A package to handle graph data structures
GraphAT Thomas LaFramboise Graph Theoretic Association Tests
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 Seth Falcon A package providing hypergraph data structures
Icens Biocore Team NPMLE for Censored and Truncated Data
idiogram Karl J. Dykema idiogram
impute Balasubramanian Narasimhan impute: Imputation for microarray data
iSPlot Elizabeth Whalen Linking Plots
KEGGSOAP J. Zhang Client-side SOAP access KEGG
limma Gordon Smyth Linear Models for Microarray Data
limmaGUI Keith Satterley GUI for limma package
LMGene Geun Cheol Lee 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
maanova Lei Wu 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
makecdfenv James W. MacDonald CDF Environment Maker
MANOR Pierre Neuvial 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
matchprobes Biocore Team 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 HyungJun Cho Misclassification Penalized Posterior Classification
MLInterfaces V. Carey Uniform interfaces to R machine learning procedures for data in Bioconductor containers
mmgmos Xuejun Liu multi-chip modified gamma Model of Oligonucleotide Signal
multtest Katherine S. Pollard Resampling-based multiple hypothesis testing
MVCClass Elizabeth Whalen Model-View-Controller (MVC) Classes
nnNorm Laurentiu A. Tarca Spatial and intensity based normalization of cDNA microarray data based on robust neural nets
nudge N. Dean Normal Uniform Differential Gene Expression detection
OCplus Alexander Ploner Operating characteristics plus sample size and local fdr for microarray experiments
OLIN Matthias Futschik Optimized local intensity-dependent normalisation of two-color microarrays
OLINgui Matthias Futschik Graphical user interface for OLIN
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
pairseqsim Witold Wolski pairwise sequence alignment similarity simple.
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
pdmclass James W. MacDonald Classification of Microarray Samples using Penalized Discriminant Methods
pgUtils Johannes Rainer Utility functions for PostgreSQL databases
pickgene Brian S. Yandell Adaptive Gene Picking for Microarray Expression Data Analysis
plgem Mattia Pelizzola Power Law Global Error Model
plier Crispin Miller Implements the Affymetrix PLIER algorithm
prada Florian Hahne Data analysis for cell-based functional assays
PROcess Xiaochun Li Ciphergen SELDI-TOF Processing
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
RBGL Li Long Interface to boost C++ graph lib
Rdbi Jianhua Zhang Generic database methods
RdbiPgSQL Jianhua Zhang PostgreSQL access
reb Karl J. Dykema Regional Expression Biases
reposTools Seth Falcon Repository tools for R
Resourcerer Jianhua Zhang Reads annotation data from TIGR Resourcerer or convert the annotation data into Bioconductor data pacakge.
rflowcyt N. Le Meur Statistical tools and data structures for analytic flow cytometry
Rgraphviz Jeff Gentry Provides plotting capabilities for R graph objects
RLMM Nusrat Rabbee A Genotype Calling Algorithm for Affymetrix SNP Arrays
RMAGEML Steffen Durinck Handling MAGEML documents
RMAPPER VJ Carey interface to
ROC Vince Carey utilities for ROC, with uarray focus
RSNPper VJ Carey interface to for SNP-related data
Ruuid Biocore Team Ruuid: Provides Universally Unique ID values
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
SBMLR Tomas Radivoyevitch SBML-R Interface and Analysis Tools
ScISI Tony Chiang In Silico Interactome
siggenes Holger Schwender SAM and Efron's empirical Bayes approaches
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
snapCGH Mike Smith Segmentation, normalisation and processing of aCGH data.
splicegear Laurent splicegear
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
stam Claudio Lottaz Structured Analysis of Microarray Data
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
twilight Stefanie Scheid Estimation of local false discovery rate
vsn Wolfgang Huber Variance stabilization and calibration for microarray data
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
y2hStat Tony Chiang Y2H Statistical Package