Bioconductor Software Packages

Bioconductor version: 2.10

Package Maintainer Title
a4 Tobias Verbeke Automated Affymetrix Array Analysis Umbrella Package
a4Base Tobias Verbeke Automated Affymetrix Array Analysis Base Package
a4Classif Tobias Verbeke Automated Affymetrix Array Analysis Classification Package
a4Core Tobias Verbeke Automated Affymetrix Array Analysis Core Package
a4Preproc Tobias Verbeke Automated Affymetrix Array Analysis Preprocessing Package
a4Reporting Tobias Verbeke 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.
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 data from aCGH experiments using parallel computing and ff objects
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
AffyCompatible Martin Morgan Affymetrix GeneChip software compatibility
affyContam V. Carey structured corruption of affymetrix cel file data
affycoretools James W. MacDonald Functions useful for those doing repetitive analyses with Affymetrix GeneChips.
AffyExpress Xuejun Arthur Li Affymetrix Quality Assessment and Analysis Tool
affyILM Myriam Kroll and Fabrice Berger Linear Model of background subtraction and the Langmuir isotherm
affyio Benjamin Milo Bolstad Tools for parsing Affymetrix data files
affylmGUI Keith Satterley GUI for affy analysis using limma package
affyPara Markus Schmidberger Parallelized preprocessing methods for Affymetrix Oligonucleotide Arrays
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
AffyRNADegradation Mario Fasold Analyze and correct probe positional bias in microarray data due to RNA degradation
AffyTiling Charles G. Danko Easy extraction of individual probes in Affymetrix tiling arrays
AGDEX Cuilan lani Gao Agreement of Differential Expression Analysis
Agi4x44PreProcess Pedro Lopez-Romero PreProcessing of Agilent 4x44 array data
AgiMicroRna Pedro Lopez-Romero Processing and Differential Expression Analysis of Agilent microRNA chips
altcdfenvs Laurent Gautier alternative CDF environments (aka probeset mappings)
annaffy Colin A. Smith Annotation tools for Affymetrix biological metadata
annotate Bioconductor Package Maintainer Annotation for microarrays
AnnotationDbi Bioconductor Package Maintainer Annotation Database Interface
AnnotationFuncs Stefan McKinnon Edwards Annotation translation functions
annotationTools Alexandre Kuhn Annotate microarrays and perform cross-species gene expression analyses using flat file databases.
anota Ola Larsson ANalysis Of Translational Activity (ANOTA).
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
ArrayExpress Audrey Kauffmann Access the ArrayExpress Microarray Database at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet
ArrayExpressHTS Angela Goncalves, Andrew Tikhonov ArrayExpress High Throughput Sequencing Processing Pipeline
arrayMvout V. Carey multivariate outlier detection for expression array QA
arrayQuality Agnes Paquet Assessing array quality on spotted arrays
arrayQualityMetrics Audrey Kauffmann Quality metrics on microarray data sets
ArrayTools Arthur Li geneChip Analysis Package
ASEB Likun Wang Predict Acetylated Lysine Sites
attract Jessica Mar Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape
BAC Raphael Gottardo Bayesian Analysis of Chip-chip experiment
BayesPeak Jonathan Cairns Bayesian Analysis of ChIP-seq Data
baySeq Thomas J. Hardcastle Empirical Bayesian analysis of patterns of differential expression in count data
BCRANK Adam Ameur Predicting binding site consensus from ranked DNA sequences
beadarray Mark Dunning Quality assessment and low-level analysis for Illumina BeadArray data
beadarraySNP Jan Oosting Normalization and reporting of Illumina SNP bead arrays
BeadDataPackR Mike Smith Compression of Illumina BeadArray data
betr Martin Aryee Identify differentially expressed genes in microarray time-course data
bgafun Iain Wallace BGAfun A method to identify specifity determining residues in protein families
BGmix Alex Lewin Bayesian models for differential gene expression
bgx Ernest Turro Bayesian Gene eXpression
BHC Rich Savage Bayesian Hierarchical Clustering
BicARE Pierre Gestraud Biclustering Analysis and Results Exploration
Biobase Bioconductor Package Maintainer Biobase: Base functions for Bioconductor
BiocCaseStudies Bioconductor Package Maintainer BiocCaseStudies: Support for the Case Studies Monograph
BiocGenerics Bioconductor Package Maintainer Generic functions for Bioconductor
biocGraph Florian Hahne Graph examples and use cases in Bioinformatics
BiocInstaller Bioconductor Package Maintainer Install/Update Bioconductor and CRAN Packages
biocViews Bioconductor Package Maintainer Categorized views of R package repositories
bioDist Bioconductor Package Maintainer Different distance measures
biomaRt Steffen Durinck Interface to BioMart databases (e.g. Ensembl, COSMIC ,Wormbase and Gramene)
BioMVCClass Elizabeth Whalen Model-View-Controller (MVC) Classes That Use Biobase
BioNet Marcus Dittrich Routines for the functional analysis of biological networks
BioSeqClass Li Hong Classification for Biological Sequences
Biostrings H. Pages String objects representing biological sequences, and matching algorithms
biovizBase Tengfei Yin Basic graphic utilities for visualization of genomic data.
birta Benedikt Zacher Bayesian Inference of Regulation of Transcriptional Activity
BitSeq Peter Glaus Transcript expression inference and differential expression analysis for RNA-seq data
BRAIN Piotr Dittwald Baffling Recursive Algorithm for Isotope distributioN calculations
BrainStars Itoshi NIKAIDO query gene expression data and plots from BrainStars (B*)
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
BUS Yuanhua Liu Gene network reconstruction
CALIB Hui Zhao Calibration model for estimating absolute expression levels from microarray data
CAMERA Carsten Kuhl Collection of annotation related methods for mass spectrometry data
CancerMutationAnalysis Simina M. Boca Cancer mutation analysis
Category Bioconductor Package Maintainer Category Analysis
categoryCompare Robert M. Flight Meta-analysis of high-throughput experiments using feature annotations
cellGrowth Julien Gagneur Fitting cell population growth models
cellHTS Ligia Bras Analysis of cell-based screens
cellHTS2 Joseph Barry Analysis of cell-based screens - revised version of cellHTS
CellNOptR T.Cokelaer R version of CellNOpt, boolean features only
CGEN William Wheeler An R package for analysis of case-control studies in genetic epidemiology
CGHbase Sjoerd Vosse 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.
charm Martin Aryee Analysis of DNA methylation data from CHARM microarrays
ChemmineR ChemmineR Team Analysis of Small Molecule and Screening Data
ChIPpeakAnno Lihua Julie Zhu Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges.
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
chopsticks Hin-Tak Leung The snp.matrix and X.snp.matrix classes
ChromHeatMap Tim F. Rayner Heat map plotting by genome coordinate
clippda Stephen Nyangoma A package for the clinical proteomic profiling data analysis
Clonality Irina Ostrovnaya Clonality testing
clst Noah Hoffman Classification by local similarity threshold
clstutils Noah Hoffman Tools for performing taxonomic assignment.
clusterProfiler Guangchuang Yu statistical analysis and visulization of functional profiles for genes and gene clusters
clusterStab James W. MacDonald Compute cluster stability scores for microarray data
CMA Christoph Bernau Synthesis of microarray-based classification
cn.farms Andreas Mitterecker cn.farms - Factor Analysis for copy number estimation
cn.mops Guenter Klambauer cn.mops - Mixture of Poissons for CNV detection in NGS data
CNAnorm Stefano Berri A normalization method for Copy Number Aberration in cancer samples
CNTools J. Zhang Convert segment data into a region by sample matrix to allow for other high level computational analyses.
cnvGSA Robert Ziman Gene Set Analysis of (Rare) Copy Number Variants
CNVtools Chris Barnes A package to test genetic association with CNV data
CoCiteStats Bioconductor Package Maintainer Different test statistics based on co-citation.
codelink Diego Diez Manipulation of Codelink Bioarrays data.
CoGAPS Elana J. Fertig, Michael F. Ochs Coordinated Gene Activity in Pattern Sets
coGPS Yingying Wei cancer outlier Gene Profile Sets
ConsensusClusterPlus Matt Wilkerson ConsensusClusterPlus
convert Yee Hwa (Jean) Yang Convert Microarray Data Objects
copa James W. MacDonald Functions to perform cancer outlier profile analysis.
Cormotif Yingying Wei Correlation Motif Fit
coRNAi Elin Axelsson Analysis of co-knock-down RNAi data
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
cqn Kasper Daniel Hansen Conditional quantile normalization
CRImage Henrik Failmezger, Yinyin Yuan CRImage a package to classify cells and calculate tumour cellularity
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.
CSAR Jose M Muino Statistical tools for the analysis of ChIP-seq data
ctc Antoine Lucas Cluster and Tree Conversion.
cummeRbund Loyal A. Goff Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
cycle Matthias Futschik Significance of periodic expression pattern in time-series data
daMA Jobst Landgrebe Efficient design and analysis of factorial two-colour microarray data
DART Katherine Lawler Denoising Algorithm based on Relevance network Topology
DAVIDQuery Roger Day Retrieval from the DAVID bioinformatics data resource into R
ddCt Jitao David Zhang The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)
DECIPHER Erik Wright Database Enabled Code for Ideal Probe Hybridization Employing R
DEDS Yuanyuan Xiao Differential Expression via Distance Summary for Microarray Data
deepSNV Moritz Gerstung Test for subclonal SNVs in deep sequencing experiments.
DEGraph Laurent Jacob Two-sample tests on a graph
DEGseq Likun Wang Identify Differentially Expressed Genes from RNA-seq data
DESeq Simon Anders Differential gene expression analysis based on the negative binomial distribution
DEXSeq Alejandro Reyes Inference of differential exon usage in RNA-Seq
DFP Rodrigo Alvarez-Glez Gene Selection
DiffBind Rory Stark Differential Binding Analysis of ChIP-Seq peak data
diffGeneAnalysis Choudary Jagarlamudi Performs differential gene expression Analysis
dks Jeffrey T. Leek The double Kolmogorov-Smirnov package for evaluating multiple testing procedures.
DNAcopy Venkatraman E. Seshan DNA copy number data analysis
domainsignatures Florian Hahne Geneset enrichment based on InterPro domain signatures
DOSE Guangchuang Yu Disease Ontology Semantic and Enrichment analysis
DTA Bjoern Schwalb Dynamic Transcriptome Analysis
dualKS Eric J. Kort Dual KS Discriminant Analysis and Classification
dyebias Philip Lijnzaad The GASSCO method for correcting for slide-dependent gene-specific dye bias
DynDoc Bioconductor Package Maintainer Dynamic document tools
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 Gregoire Pau Image processing toolbox for R
ecolitk Laurent Gautier Meta-data and tools for E. coli
EDASeq Davide Risso Exploratory Data Analysis and Normalization for RNA-Seq
edgeR Mark Robinson, Davis McCarthy, Yunshun Chen, Gordon Smyth Empirical analysis of digital gene expression data in R
eisa Gabor Csardi Expression data analysis via the Iterative Signature Algorithm
ENVISIONQuery Alex Lisovich, Roger Day Retrieval from the ENVISION bioinformatics data portal into R
ExiMiR Sylvain Gubian R functions for the normalization of Exiqon miRNA array data
exomeCopy Michael Love CNV detection from exome sequencing read depth
explorase Michael Lawrence GUI for exploratory data analysis of systems biology data
ExpressionView Gabor Csardi Visualize biclusters identified in gene expression data
externalVector Bioconductor Package Maintainer Vector objects for R with external storage
fabia Sepp Hochreiter FABIA: Factor Analysis for Bicluster Acquisition
factDesign Denise Scholtens Factorial designed microarray experiment analysis
farms Djork-Arne Clevert FARMS - Factor Analysis for Robust Microarray Summarization
fastseg Guenter Klambauer fastseg - a fast segmentation algorithm
fdrame Effi Kenigsberg FDR adjustments of Microarray Experiments (FDR-AME)
ffpe Levi Waldron Quality assessment and control for FFPE microarray expression data
flagme Mark Robinson Analysis of Metabolomics GC/MS Data
flowClust Raphael Gottardo Clustering for Flow Cytometry
flowCore M.Jiang flowCore: Basic structures for flow cytometry data
flowFlowJo John J. Gosink Tools for extracting information from a FlowJo workspace and working with the data in the flowCore paradigm.
flowFP Herb Holyst Fingerprinting for Flow Cytometry
flowMeans Nima Aghaeepour Non-parametric Flow Cytometry Data Gating
flowMerge Greg Finak Cluster Merging for Flow Cytometry Data
flowPhyto David M. Schruth Methods for Continuous Flow Cytometry
flowPlots N. Hawkins flowPlots: analysis plots and data class for gated flow cytometry data
flowQ Mike Jiang Quality control for flow cytometry
flowStats Greg Finak and Mike Jiang Statistical methods for the analysis of flow cytometry data
flowTrans Greg Finak Parameter Optimization for Flow Cytometry Data Transformation
flowType Nima Aghaeepour Phenotyping Flow Cytometry Assays
flowUtils Nishant Gopalakrishnan Utilities for flow cytometry
flowViz Mike Jiang Visualization for flow cytometry
flowWorkspace Greg Finak Import flowJo Workspaces into BioConductor and replicate flowJo gating with flowCore
frma Matthew N. McCall Frozen RMA and Barcode
frmaTools Matthew N. McCall Frozen RMA Tools
gaga David Rossell GaGa hierarchical model for high-throughput data analysis
gage Weijun Luo Generally Applicable Gene-set Enrichment for Pathway Analysis
gaggle Christopher Bare Broadcast data between R and Gaggle
gaia S. Morganella GAIA: An R package for genomic analysis of significant chromosomal aberrations.
gcrma Z. Wu Background Adjustment Using Sequence Information
genArise IFC Development Team Microarray Analysis tool
gene2pathway Holger Froehlich Prediction of KEGG pathway membership for individual genes based on InterPro domain signatures
GeneAnswers Gang Feng, Pan Du and Tian Xia Integrated Interpretation of Genes
GeneExpressionSignature Yang Cao, Fei Li Gene Expression Signature based Similarity Metric
genefilter Bioconductor Package Maintainer genefilter: methods for filtering genes from microarray experiments
genefu Benjamin Haibe-Kains, Markus Schroeder Relevant Functions for Gene Expression Analysis, Especially in Breast Cancer.
GeneGA Zhenpeng Li Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm
GeneGroupAnalysis Alejandro Quiroz-Zarate Gene Functional Class Analysis
GeneMeta Bioconductor Package Maintainer MetaAnalysis for High Throughput Experiments
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
GeneSelectMMD Weiliang Qiu Gene selection based on the marginal distributions of gene profiles that characterized by a mixture of three-component multivariate distributions
GeneSelector Martin Slawski Stability and Aggregation of ranked gene lists
GeneticsDesign The R Genetics Project Functions for designing genetics studies
GeneticsPed David Henderson Pedigree and genetic relationship functions
genoCN Wei Sun genotyping and copy number study tools
GenomeGraphs Steffen Durinck Plotting genomic information from Ensembl
genomeIntervals Julien Gagneur Operations on genomic intervals
genomes Chris Stubben Genome sequencing project metadata
GenomicFeatures Bioconductor Package Maintainer Tools for making and manipulating transcript centric annotations
GenomicRanges Bioconductor Package Maintainer Representation and manipulation of genomic intervals
Genominator James Bullard Analyze, manage and store genomic data
genoset Peter M. Haverty Provides classes similar to ExpressionSet for copy number analysis
GEOmetadb Jack Zhu A compilation of metadata from NCBI GEO
GEOquery Sean Davis Get data from NCBI Gene Expression Omnibus (GEO)
GEOsubmission Alexandre Kuhn Prepares microarray data for submission to GEO
GEWIST Wei Q. Deng Gene Environment Wide Interaction Search Threshold
GGBase VJ Carey GGBase infrastructure for genetics of gene expression package GGtools
ggbio Tengfei Yin Static visualization for genomic data.
GGtools VJ Carey software and data for analyses in genetics of gene expression
girafe J. Toedling Genome Intervals and Read Alignments for Functional Exploration
GLAD Philippe Hupe Gain and Loss Analysis of DNA
GlobalAncova Manuela Hummel Calculates a global test for differential gene expression between groups
globaltest Jelle Goeman Testing groups of covariates/features for association with a response variable, with applications to gene set testing
GOFunction Zheng Guo GO-function: deriving biologcially relevant functions from statistically significant functions
goProfiles Alex Sanchez goProfiles: an R package for the statistical analysis of functional profiles
GOSemSim Guangchuang Yu GO-terms Semantic Similarity Measures
goseq Matthew Young Gene Ontology analyser for RNA-seq and other length biased data
GOstats Bioconductor Package Maintainer Tools for manipulating GO and microarrays.
goTools Agnes Paquet Functions for Gene Ontology database
gpls Bioconductor Package Maintainer Classification using generalized partial least squares
gprege Alfredo A. Kalaitzis Gaussian Process Ranking and Estimation of Gene Expression time-series
graph Seth Falcon 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
GRENITS Edward Morrissey Gene Regulatory Network Inference Using Time Series
GSEABase Bioconductor Package Maintainer Gene set enrichment data structures and methods
GSEAlm Assaf Oron Linear Model Toolset for Gene Set Enrichment Analysis
GSRI Julian Gehring Gene Set Regulation Index
GSVA Justin Guinney Gene Set Variation Analysis
Gviz Florian Hahne Plotting data and annotation information along genomic coordinates
gwascat VJ Carey representing and modeling data in the NHGRI GWAS catalog
GWASTools Stephanie M. Gogarten Tools for Genome Wide Association Studies
Harshlight Maurizio Pellegrino A "corrective make-up" program for microarray chips
Heatplus Alexander Ploner Heatmaps with row and/or column covariates and colored clusters
HELP Reid F. Thompson Tools for HELP data analysis
HEM HyungJun Cho Heterogeneous error model for identification of differentially expressed genes under multiple conditions
HilbertVis Simon Anders Hilbert curve visualization
HilbertVisGUI Simon Anders HilbertVisGUI
HiTC N. Servant High Throughput Chromosome Conformation Capture analysis
hopach Katherine S. Pollard Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
HTqPCR Heidi Dvinge Automated analysis of high-throughput qPCR data
HTSanalyzeR Xin Wang Gene set over-representation, enrichment and network analyses for high-throughput screens
htSeqTools Oscar Reina Quality Control, Visualization and Processing for High-Throughput Sequencing data
HybridMTest Demba Fofana Hybrid Multiple Testing
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
iBBiG Aedin Culhane Iterative Binary Biclustering of Genesets
ibh Kircicegi Korkmaz Interaction Based Homogeneity for Evaluating Gene Lists
Icens Bioconductor Package Maintainer NPMLE for Censored and Truncated Data
iChip Qianxing Mo Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models
idiogram Karl J. Dykema idiogram
IdMappingAnalysis Alex Lisovich, Roger Day ID Mapping Analysis
IdMappingRetrieval Alex Lisovich, Roger Day ID Mapping Data Retrieval
iFlow Kyongryun Lee GUI based visualization for flow cytometry
imageHTS Gregoire Pau Analysis of high-throughput microscopy-based screens
impute Balasubramanian Narasimhan impute: Imputation for microarray data
inSilicoDb Jonatan Taminau, David Steenhoff Access to the InSilico Database
inSilicoMerging Jonatan Taminau, Stijn Meganck, Cosmin Lazar Collection of Merging Techniques for Gene Expression Data
inveRsion Alejandro Caceres Inversions in genotype data
iontree Mingshu Cao Data management and analysis of ion trees from ion-trap mass spectrometry
IPPD Martin Slawski Isotopic peak pattern deconvolution for Protein Mass Spectrometry by template matching
IRanges Bioconductor Package Maintainer Infrastructure for manipulating intervals on sequences
iSeq Qianxing Mo Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising Models
isobar Florian P Breitwieser Analysis and quantitation of isobarically tagged MSMS proteomics data
IsoGeneGUI Setia Pramana A graphical user interface to conduct a dose-response analysis of microarray data
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
joda Ewa Szczurek JODA algorithm for quantifying gene deregulation using knowledge
KCsmart Jorma de Ronde Multi sample aCGH analysis package using kernel convolution
KEGGgraph Jitao David Zhang KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
keggorthology VJ Carey graph support for KO, KEGG Orthology
KEGGSOAP Bioconductor Package Maintainer Client-side SOAP access KEGG
lapmix Yann Ruffieux Laplace Mixture Model in Microarray Experiments
LBE Cyril Dalmasso Estimation of the false discovery rate.
les Julian Gehring Identifying Differential Effects in Tiling Microarray Data
limma Gordon Smyth Linear Models for Microarray Data
limmaGUI Keith Satterley GUI for limma package
LiquidAssociation Yen-Yi Ho LiquidAssociation
LMGene Blythe Durbin-Johnson LMGene Software for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays
logicFS Holger Schwender Identification of SNP Interactions
logitT Tobias Guennel logit-t Package
lol Yinyin Yuan Lots Of Lasso
LPE Nitin Jain Methods for analyzing microarray data using Local Pooled Error (LPE) method
LPEadj Carl Murie A correction of the local pooled error (LPE) method to replace the asymptotic variance adjustment with an unbiased adjustment based on sample size.
lumi Pan Du BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
LVSmiRNA Stefano Calza LVS normalization for Agilent miRNA data
maanova Keith Sheppard 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
MANOR Pierre Neuvial CGH Micro-Array NORmalization
manta David M. Schruth Microbial Assemblage Normalized Transcript Analysis
MantelCorr Brian Steinmeyer Compute Mantel Cluster Correlations
marray Yee Hwa (Jean) Yang Exploratory analysis for two-color spotted microarray data
maSigPro Maria Jose Nueda Significant Gene Expression Profile Differences in Time Course Microarray Data
maskBAD Michael Dannemann Masking probes with binding affinity differences
MassArray Reid F. Thompson Analytical Tools for MassArray Data
MassSpecWavelet Pan Du Mass spectrum processing by wavelet-based algorithms
MBCB Jeff Allen MBCB (Model-based Background Correction for Beadarray)
mBPCR P.M.V. Rancoita Bayesian Piecewise Constant Regression for DNA copy number estimation
mcaGUI Wade K. Copeland Microbial Community Analysis GUI
MCRestimate Marc Johannes Misclassification error estimation with cross-validation
mdqc Gabriela Cohen-Freue Mahalanobis Distance Quality Control for microarrays
MeasurementError.cor Beiying Ding Measurement Error model estimate for correlation coefficient
MEDIPS Lukas Chavez MeDIP-Seq data analysis
MEDME Mattia Pelizzola Modelling Experimental Data from MeDIP Enrichment
MergeMaid Xiaogang Zhong Merge Maid
metaArray Hyungwon Choi Integration of Microarray Data for Meta-analysis
metahdep John R. Stevens Hierarchical Dependence in Meta-Analysis
methVisual Arie Zackay Methods for visualization and statistics on DNA methylation data
methylumi Sean Davis Handle Illumina methylation data
Mfuzz Matthias Futschik Soft clustering of time series gene expression data
mgsa Sebastian Bauer Model-based gene set analysis
MiChip Jonathon Blake MiChip Parsing and Summarizing Functions
microRNA "James F. Reid" Data and functions for dealing with microRNAs
minet Patrick E. Meyer Mutual Information NETworks
minfi Kasper Daniel Hansen Analyze Illumina's 450k methylation arrays
MinimumDistance Moiz Bootwalla, Robert B Scharpf A package for de novo CNV detection in case-parent trios
MiPP Sukwoo Kim Misclassification Penalized Posterior Classification
miRNApath James M. Ward miRNApath: Pathway Enrichment for miRNA Expression Data
MLInterfaces V. Carey Uniform interfaces to R machine learning procedures for data in Bioconductor containers
MLP Tobias Verbeke MLP
MmPalateMiRNA Guy Brock Murine Palate miRNA Expression Analysis
mosaics Dongjun Chung MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)
motifRG Zizhen Yao A package for discriminative motif discovery, designed for high throughput sequencing dataset
MotIV Eloi Mercier, Raphael Gottardo Motif Identification and Validation
MSnbase Laurent Gatto MSnbase: Base Functions and Classes for MS-based Proteomics
Mulcom Claudio Isella Calculates Mulcom test
multiscan Mizanur Khondoker R package for combining multiple scans
multtest Katherine S. Pollard Resampling-based multiple hypothesis testing
MVCClass Elizabeth Whalen Model-View-Controller (MVC) Classes
mzR Bernd Fischer, Steffen Neumann, Laurent Gatto parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)
NarrowPeaks Pedro Madrigal Functional Principal Component Analysis to Narrow Down Transcription Factor Binding Site Candidates
ncdfFlow M. Jiang ncdfFlow: A package that provides ncdf based storage for flow cytometry data.
NCIgraph Laurent Jacob Pathways from the NCI Pathways Database
nem Holger Froehlich Nested Effects Models to reconstruct phenotypic hierarchies
netresponse Leo Lahti NetResponse: functional network analysis
nnNorm Adi Laurentiu Tarca Spatial and intensity based normalization of cDNA microarray data based on robust neural nets
NormqPCR James Perkins Functions for normalisation of RT-qPCR data
NTW Yuanhua Liu Predict gene network using an Ordinary Differential Equation (ODE) based method
nucleR Oscar Flores Nucleosome positioning package for R
nudge N. Dean Normal Uniform Differential Gene Expression detection
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
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
oneChannelGUI Raffaele A Calogero A graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops.
ontoCAT Natalja Kurbatova Ontology traversal and search
OrderedList Claudio Lottaz Similarities of Ordered Gene Lists
OTUbase Daniel Beck Provides structure and functions for the analysis of OTU data
OutlierD Sukwoo Kim Outlier detection using quantile regression on the M-A scatterplots of high-throughput data
PAnnBuilder Li Hong Protein annotation data package builder
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
parody VJ Carey Parametric And Resistant Outlier DYtection
pathRender Li Long Render molecular pathways
PatientGeneSets Simina M. Boca Patient-oriented gene-set analysis
pcaGoPromoter Morten Hansen pcaGoPromoter is used to analyze DNA micro array data
pcaMethods Wolfram Stacklies A collection of PCA methods.
pcot2 Sarah Song Principal Coordinates and Hotelling's T-Square method
PCpheno Nolwenn Le Meur Phenotypes and cellular organizational units
pdInfoBuilder Benilton Carvalho 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
phenoDist Xian Zhang Phenotypic distance measures
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.
phyloseq Paul J. McMurdie Handling and analysis of high-throughput phylogenetic sequence data.
pickgene Brian S. Yandell Adaptive Gene Picking for Microarray Expression Data Analysis
PICS Arnaud Droit Probabilistic inference of ChIP-seq
PING Xuekui Zhang, Raphael Gottardo, Sangsoon Woo, Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data
pint Olli-Pekka Huovilainen Pairwise INTegration of functional genomics data
pkgDepTools Seth Falcon Package Dependency Tools
plateCore Errol Strain Statistical tools and data structures for plate-based flow cytometry
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
PLPE Soo-heang Eo Local Pooled Error Test for Differential Expression with Paired High-throughput Data
plw Magnus Astrand Probe level Locally moderated Weighted t-tests.
ppiStats Tony Chiang Protein-Protein Interaction Statistical Package
prada Florian Hahne Data analysis for cell-based functional assays
PREDA Francesco Ferrari Position RElated Data Anlysis
predictionet Benjamin Haibe-Kains, Catharina Olsen Inference for predictive networks designed for (but not limited to) genomic data
preprocessCore Benjamin Milo Bolstad A collection of pre-processing functions
PROcess Xiaochun Li Ciphergen SELDI-TOF Processing
procoil Ulrich Bodenhofer Prediction of Oligomerization of Coiled Coil Proteins
PROMISE Stan Pounds, Xueyuan Cao PRojection Onto the Most Interesting Statistical Evidence
puma Richard Pearson Propagating Uncertainty in Microarray Analysis
pvac Jun Lu, Pierre R. Bushel PCA-based gene filtering for Affymetrix arrays
qpcrNorm Jessica Mar Data-driven normalization strategies for high-throughput qPCR data.
qpgraph Robert Castelo Reverse engineering of molecular regulatory networks with qp-graphs
qrqc Vince Buffalo Quick Read Quality Control
QUALIFIER Mike Jiang Qualitiy Control of Gated Flow Cytometry Experiments
quantsmooth Jan Oosting Quantile smoothing and genomic visualization of array data
qvalue John D. Storey Q-value estimation for false discovery rate control
r3Cseq Supat Thongjuea 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.
rama Raphael Gottardo Robust Analysis of MicroArrays
RamiGO Markus Schroeder AmiGO visualize R interface
randPack Robert Gentleman Randomization routines for Clinical Trials
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 Bioconductor Package Maintainer An interface to the BOOST graph library
RBioinf Robert Gentleman RBioinf
rbsurv Soo-heang Eo Robust likelihood-based survival modeling with microarray data
RCASPAR Douaa Mugahid, Lars Kaderali A package for survival time prediction based on a piecewise baseline hazard Cox regression model.
RchyOptimyx Adrin Jalali, Nima Aghaeepour Optimyzed Cellular Hierarchies for Flow Cytometry
RCytoscape Paul Shannon Display and manipulate graphs in Cytoscape
Rdisop Steffen Neumann Decomposition of Isotopic Patterns
RDRToolbox Christoph Bartenhagen A package for nonlinear dimension reduction with Isomap and LLE.
ReactomePA Guangchuang Yu Reactome Pathway Analysis
ReadqPCR James Perkins Read qPCR data
reb Karl J. Dykema Regional Expression Biases
RedeR Mauro Castro Bridging the gap between hierarchical network representation and functional analysis.
REDseq Lihua Julie Zhu Analysis of high-throughput sequencing data processed by restriction enzyme digestion
RefPlus Kai-Ming Chang A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods.
Repitools Mark Robinson Epigenomic tools
ReQON Christopher Cabanski Recalibrating Quality Of Nucleotides
Resourcerer Jianhua Zhang Reads annotation data from TIGR Resourcerer or convert the annotation data into Bioconductor data pacakge.
rGADEM Arnaud Droit de novo motif discovery
Rgraphviz Kasper Hansen Provides plotting capabilities for R graph objects
rhdf5 Bernd Fischer HDF5 interface to R
rHVDM Martino Barenco Hidden Variable Dynamic Modeling
Ringo J. Toedling R Investigation of ChIP-chip Oligoarrays
RLMM Nusrat Rabbee A Genotype Calling Algorithm for Affymetrix SNP Arrays
Rmagpie Camille Maumet MicroArray Gene-expression-based Program In Error rate estimation
RMAPPER Heike Sichtig, Alberto Riva R interface to the MAPPER database of transcription factor binding sites
rMAT Arnaud Droit and Raphael Gottardo R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data.
RmiR Francesco Favero Package to work with miRNAs and miRNA targets with R
RNAinteract Bernd Fischer Estimate Pairwise Interactions from multidimensional features
RNAither Nora Rieber Statistical analysis of high-throughput RNAi screens
rnaSeqMap Michal Okoniewski rnaSeq secondary analyses
ROC Vince Carey utilities for ROC, with uarray focus
Rolexa Jacques Rougemont Statistical analysis of Solexa sequencing data
RPA Leo Lahti RPA: Robust Probabilistic Averaging for probe-level analysis
RpsiXML Jitao David Zhang R interface to PSI-MI 2.5 files
rqubic Jitao David Zhang Qualitative biclustering algorithm for expression data analysis in R
Rsamtools Bioconductor Package Maintainer Binary alignment (BAM), variant call (BCF), or tabix file import
rsbml Michael Lawrence R support for SBML, using libsbml
Rsubread Wei Shi Rsubread: a super fast, sensitive and accurate read aligner for mapping next-generation sequencing reads
RTCA Jitao David Zhang Open-source toolkit to analyse data from xCELLigence System (RTCA)
RTopper Luigi Marchionni This package is designed to perform Gene Set Analysis across multiple genomic platforms
rtracklayer Michael Lawrence R interface to genome browsers and their annotation tracks
Rtreemix Jasmina Bogojeska Rtreemix: Mutagenetic trees mixture models.
RWebServices Martin Morgan Expose R functions as web services through Java/Axis/Apache
safe William T. Barry Significance Analysis of Function and Expression
sagenhaft Tim Beissbarth Collection of functions for reading and comparing SAGE libraries
SAGx Per Broberg, Statistical Analysis of the GeneChip
SamSPECTRAL Habil Zare Identifies cell population in flow cytometry data.
SBMLR Tomas Radivoyevitch SBML-R Interface and Analysis Tools
ScISI Tony Chiang In Silico Interactome
segmentSeq Thomas J. Hardcastle Methods for identifying small RNA loci from high-throughput sequencing data
seqbias Daniel Jones Estimation of per-position bias in high-throughput sequencing data
seqLogo Oliver Bembom Sequence logos for DNA sequence alignments
ShortRead Bioconductor Package Maintainer Classes and methods for high-throughput short-read sequencing data.
sigaR Wessel N. van Wieringen statistics for integrative genomics analyses in R
siggenes Holger Schwender Multiple testing using SAM and Efron's empirical Bayes approaches
sigPathway Weil Lai Pathway Analysis
SIM Maarten van Iterson Integrated Analysis on two human genomic datasets
simpleaffy Crispin Miller Very simple high level analysis of Affymetrix data
sizepower Weiliang Qiu Sample Size and Power Calculation in Micorarray Studies
SJava Martin Morgan The Omegahat interface for R and Java.
SLGI Nolwenn Le Meur Synthetic Lethal Genetic Interaction
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.
snm Brig Mecham Supervised Normalization of Microarrays
SNPchip Robert Scharpf Visualizations for copy number alterations
snpStats David Clayton SnpMatrix and XSnpMatrix classes and methods
spade Michael Linderman SPADE -- An analysis and visualization tool for Flow Cytometry
SpeCond Florence Cavalli Condition specific detection from expression data
SPIA Adi Laurentiu Tarca Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
spikeLI Enrico Carlon Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool
spkTools Matthew N McCall Methods for Spike-in Arrays
splicegear Laurent Gautier splicegear
splots Wolfgang Huber Visualization of high-throughput assays in microtitre plate or slide format
spotSegmentation Chris Fraley Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots
SQUADD Martial Sankar Add-on of the SQUAD Software
SRAdb Jack Zhu A compilation of metadata from NCBI SRA and tools
sscore Richard Kennedy S-Score Algorithm for Affymetrix Oligonucleotide Microarrays
ssize Gregory R. Warnes Estimate Microarray Sample Size
SSPA Maarten van Iterson Sample Size and Power Analysis for Microarray Data
Starr Benedikt Zacher Simple tiling array analysis of Affymetrix ChIP-chip data
stepNorm Yuanyuan Xiao Stepwise normalization functions for cDNA microarrays
stepwiseCM Askar Obulkasim Stepwise Classification of Cancer Samples using Clinical and Molecular Data
Streamer Martin Morgan Enabling stream processing of large files
survcomp Benjamin Haibe-Kains, Markus Schroeder, Catharina Olsen Performance Assessment and Comparison for Survival Analysis
sva Jeffrey T. Leek Surrogate Variable Analysis
TargetSearch Alvaro Cuadros-Inostroza A package for the analysis of GC-MS metabolite profiling data.
TDARACNE Zoppoli Pietro Network reverse engineering from time course data.
TEQC Manuela Hummel Quality control for target capture experiments
ternarynet Matthew N. McCall Ternary Network Estimation
tigre Antti Honkela Transcription factor Inference through Gaussian process Reconstruction of Expression
tilingArray Zhenyu Xu Transcript mapping with 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
trigger John D. Storey Transcriptional Regulatory Inference from Genetics of Gene ExpRession
tspair Jeffrey T. Leek Top Scoring Pairs for Microarray Classification
TSSi Julian Gehring Transcription Start Site Identification
TurboNorm Maarten van Iterson A fast scatterplot smoother suitable for microarray normalization
tweeDEseq Juan R Gonzalez RNA-seq data analysis using the Poisson-Tweedie family of distributions
twilight Stefanie Scheid Estimation of local false discovery rate
TypeInfo Duncan Temple Lang Optional Type Specification Prototype
VanillaICE Robert Scharpf A Hidden Markov Model for high throughput genotyping arrays
VariantAnnotation Valerie Obenchain Annotation of Genetic Variants
vbmp Nicola Lama Variational Bayesian Multinomial Probit Regression
Vega Sandro Morganella An R package for copy number data segmentation
VegaMC Sandro Morganella VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer
virtualArray Andreas Heider Build virtual array from different microarray platforms
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
widgetTools Jianhua Zhang Creates an interactive tcltk widget
xcms Ralf Tautenhahn LC/MS and GC/MS Data Analysis
XDE Robert Scharpf XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression
xmapbridge Tim Yates Export plotting files to the xmapBridge for visualisation in X:Map
xmapcore Tim Yates Core access to the xmap database (installed separately)
xps Christian Stratowa Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays
yaqcaffy Laurent Gatto Affymetrix expression data quality control and reproducibility analysis
zlibbioc Bioconductor Package Maintainer An R packaged zlib-1.2.5

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