Bioconductor Software Packages

Bioconductor version: 2.14

Package Maintainer Title
a4 Tobias Verbeke, Willem Ligtenberg Automated Affymetrix Array Analysis Umbrella Package
a4Base Tobias Verbeke, Willem Ligtenberg Automated Affymetrix Array Analysis Base Package
a4Classif Tobias Verbeke, Willem Ligtenberg Automated Affymetrix Array Analysis Classification Package
a4Core Tobias Verbeke, Willem Ligtenberg Automated Affymetrix Array Analysis Core Package
a4Preproc Tobias Verbeke, Willem Ligtenberg Automated Affymetrix Array Analysis Preprocessing Package
a4Reporting Tobias Verbeke, Willem Ligtenberg 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.
ABSSeq Wentao Yang ABSSeq: a new RNA-Seq analysis method based on absolute expression differences and generalized Poisson model
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
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
agilp Benny Chain Agilent expression array processing package
AgiMicroRna Pedro Lopez-Romero Processing and Differential Expression Analysis of Agilent microRNA chips
AllelicImbalance Jesper R Gadin Investigates allele specific expression
alsace Ron Wehrens ALS for the Automatic Chemical Exploration of mixtures
altcdfenvs Laurent Gautier alternative CDF environments (aka probeset mappings)
ampliQueso Michal Okoniewski Analysis of amplicon enrichment panels
annaffy Colin A. Smith Annotation tools for Affymetrix biological metadata
annmap Tim Yates Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.
annotate Bioconductor Package Maintainer Annotation for microarrays
AnnotationDbi Bioconductor Package Maintainer Annotation Database Interface
AnnotationForge Bioconductor Package Maintainer Code for Building Annotation Database Packages
AnnotationFuncs Stefan McKinnon Edwards Annotation translation functions
AnnotationHub Marc Carlson A client for retrieving Bioconductor objects from AnnotationHub
annotationTools Alexandre Kuhn Annotate microarrays and perform cross-species gene expression analyses using flat file databases.
anota Ola Larsson ANalysis Of Translational Activity (ANOTA).
antiProfiles Hector Corrada Bravo Implementation of gene expression anti-profiles
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 Ibrahim Emam 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
ArrayTV Eitan Halper-Stromberg Implementation of wave correction for arrays
ARRmNormalization Jean-Philippe Fortin Adaptive Robust Regression normalization for Illumina methylation data
ASEB Likun Wang Predict Acetylated Lysine Sites
asmn Anna Decker All sample mean normalization.
ASSET William Wheeler An R package for subset-based association analysis of heterogeneous traits and subtypes
ASSIGN Ying Shen Adaptive Signature Selection and InteGratioN (ASSIGN)
AtlasRDF James Malone Gene Expression Atlas query and gene set enrichment package.
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
BADER Andreas Neudecker Bayesian Analysis of Differential Expression in RNA Sequencing Data
BAGS Alejandro Quiroz-Zarate A Bayesian Approach for Geneset Selection
BaseSpaceR Adrian Alexa R SDK for BaseSpace RESTful API
Basic4Cseq Carolin Walter Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
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
BEAT Kemal Akman BEAT - BS-Seq Epimutation Analysis Toolkit
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
BiGGR Anand K. Gavai, Hannes Hettling Constraint based modeling in R using metabolic reconstruction databases.
bigmemoryExtras Peter M. Haverty An extension of the bigmemory package with added safety, convenience, and a factor class.
bioassayR Tyler Backman R library for Bioactivity analysis
Biobase Bioconductor Package Maintainer Biobase: Base functions for Bioconductor
BiocCaseStudies Bioconductor Package Maintainer BiocCaseStudies: Support for the Case Studies Monograph
BiocCheck Bioconductor Package Maintainer Bioconductor-specific package checks
BiocGenerics Bioconductor Package Maintainer S4 generic functions for Bioconductor
biocGraph Florian Hahne Graph examples and use cases in Bioinformatics
BiocInstaller Bioconductor Package Maintainer Install/Update Bioconductor and CRAN Packages
BiocParallel Bioconductor Package Maintainer Bioconductor facilities for parallel evaluation
BiocStyle Bioconductor Package Maintainer Standard styles for vignettes and other Bioconductor documents
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
biomvRCNS Yang Du Copy Number study and Segmentation for multivariate biological data
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
biosvd Anneleen Daemen, Matthew Brauer Package for high-throughput data processing, outlier detection, noise removal and dynamic modeling
biovizBase Tengfei Yin 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) preserving degree distribution (or marginal totals).
birta Benedikt Zacher, Holger Froehlich Bayesian Inference of Regulation of Transcriptional Activity
BiSeq Katja Hebestreit Processing and analyzing bisulfite sequencing data
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
bsseq Kasper Daniel Hansen Analyze, manage and store bisulfite sequencing data
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
bumphunter Rafael A. Irizarry Bump Hunter
BUS Yuanhua Liu Gene network reconstruction
CAFE Sander Bollen Chromosmal Aberrations Finder in Expression data
CAGEr Vanja Haberle Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
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
cancerclass Daniel Kosztyla Development and validation of diagnostic tests from high-dimensional molecular data
CancerMutationAnalysis Simina M. Boca Cancer mutation analysis
casper David Rossell Characterization of Alternative Splicing based on Paired-End Reads
Category Bioconductor Package Maintainer Category Analysis
categoryCompare Robert M. Flight Meta-analysis of high-throughput experiments using feature annotations
ccrepe Emma Schwager,Craig Bielski, George Weingart ccrepe_and_nc.score
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 Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data.
CexoR Pedro Madrigal An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates
CGEN William Wheeler 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 Tiffany Morris Chip Analysis Methylation Pipeline for Illumina HumanMethylation450
charm Peter Murakami Analysis of DNA methylation data from CHARM microarrays
ChemmineOB Kevin Horan R interface to a subset of OpenBabel functionalities
ChemmineR ChemmineR Team Cheminformatics Toolkit for R
chimera Raffaele A Calogero A package for secondary analysis of fusion products
chipenrich Ryan P. Welch Gene set enrichment for ChIP-seq peak 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.
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
chroGPS Oscar Reina chroGPS: visualizing the epigenome
ChromHeatMap Tim F. Rayner Heat map plotting by genome coordinate
cisPath Likun Wang Visualization and management of the protein-protein interaction networks.
cleanUpdTSeq Sarah Sheppard ; Jianhong Ou ; Lihua Julie Zhu This package classifies putative polyadenylation sites as true or false/internally oligodT primed.
cleaver Sebastian Gibb Cleavage of polypeptide sequences
clippda Stephen Nyangoma A package for the clinical proteomic profiling data analysis
clipper Paolo Martini Gene set analysis exploiting pathway topology
Clomial Habil Zare Infers clonal composition of a tumor
Clonality Irina Ostrovnaya Clonality testing
clonotypeR Charles Plessy High throughput analysis of T cell antigen receptor sequences
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
CNEr Ge Tan CNE detection and visualization.
CNORdt A. MacNamara Add-on to CellNOptR: Discretized time treatments
CNORfeeder F.Eduati Integration of CellNOptR to add missing links
CNORfuzzy T. Cokelaer Addon to CellNOptR: Fuzzy Logic
CNORode David Henriques 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.
cnvGSA Robert Ziman Gene Set Analysis of (Rare) Copy Number Variants
CNVrd2 Hoang Tan Nguyen CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.
CNVtools Chris Barnes A package to test genetic association with CNV data
cobindR Manuela Benary Finding Co-occuring motifs of transcription factor binding sites
CoCiteStats Bioconductor Package Maintainer Different test statistics based on co-citation.
codelink Diego Diez Manipulation of Codelink microarray data.
CoGAPS Elana J. Fertig, Michael F. Ochs Coordinated Gene Activity in Pattern Sets
coGPS Yingying Wei cancer outlier Gene Profile Sets
COHCAP Charles Warden CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data
COMPASS Kevin Ushey Combinatorial Polyfunctionality Analysis of Single Cells
compcodeR Charlotte Soneson RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods
CompGO Ash Waardenberg An R pipeline for .bed file annotation, comparing GO term enrichment between gene sets and data visualisation
ConsensusClusterPlus Matt Wilkerson ConsensusClusterPlus
convert Yee Hwa (Jean) Yang Convert Microarray Data Objects
copa James W. MacDonald Functions to perform cancer outlier profile analysis.
COPDSexualDimorphism J Fah Sathirapongsasuti Sexual dimorphic and COPD differential analysis for gene expression and methylation.
copynumber Gro Nilsen Segmentation of single- and multi-track copy number data by penalized least squares regression.
CopyNumber450k Simon Papillon-Cavanagh R package for calling CNV from Illumina 450k methylation microarrays
Cormotif Yingying Wei Correlation Motif Fit
CorMut Zhenpeng Li Detect the correlated mutations based on selection pressure
coRNAi Elin Axelsson Analysis of co-knock-down RNAi data
CORREP Dongxiao Zhu Multivariate Correlation Estimator and Statistical Inference Procedures.
CoverageView Ernesto Lowy Coverage visualization package for R
cqn Kasper Daniel Hansen Conditional quantile normalization
CRImage Henrik Failmezger, Yinyin Yuan CRImage a package to classify cells and calculate tumour cellularity
CRISPRseek Lihua Julie Zhu Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems
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
CSSP Chandler Zuo ChIP-Seq Statistical Power
ctc Antoine Lucas Cluster and Tree Conversion.
cummeRbund Loyal A. Goff Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
customProDB xiaojing wang Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search.
cycle Matthias Futschik Significance of periodic expression pattern in time-series data
dagLogo Jianhong Ou dagLogo
daMA Jobst Landgrebe Efficient design and analysis of factorial two-colour microarray data
DART Katherine Lawler Denoising Algorithm based on Relevance network Topology
DASiR Oscar Flores, Anna Mantsoki Distributed Annotation System in R
DAVIDQuery Roger Day Retrieval from the DAVID bioinformatics data resource into R
DBChIP Kun Liang Differential Binding of Transcription Factor with ChIP-seq
ddCt Jitao David Zhang The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)
ddgraph Robert Stojnic Distinguish direct and indirect interactions with Graphical Modelling
DECIPHER Erik Wright Database Enabled Code for Ideal Probe Hybridization Employing R
DeconRNASeq Ting Gong Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq data
DEDS Yuanyuan Xiao Differential Expression via Distance Summary for Microarray Data
deepSNV Moritz Gerstung Detection of 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
deltaGseg Diana Low deltaGseg
DESeq Simon Anders Differential gene expression analysis based on the negative binomial distribution
DESeq2 Michael Love Differential gene expression analysis based on the negative binomial distribution
DEXSeq Alejandro Reyes Inference of differential exon usage in RNA-Seq
dexus Guenter Klambauer DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates
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
DirichletMultinomial Martin Morgan Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
dks Jeffrey T. Leek The double Kolmogorov-Smirnov package for evaluating multiple testing procedures.
DMRcate Tim Peters Illumina 450K methylation array spatial analysis methods
DMRforPairs Martin Rijlaarsdam DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles
DNAcopy Venkatraman E. Seshan DNA copy number data analysis
DNaseR Pedro Madrigal DNase I footprinting analysis of DNase-seq data
domainsignatures Florian Hahne Geneset enrichment based on InterPro domain signatures
DOSE Guangchuang Yu Disease Ontology Semantic and Enrichment analysis
DriverNet Jiarui Ding Drivernet: uncovering somatic driver mutations modulating transcriptional networks in cancer
DrugVsDisease j. Saez-Rodriguez Comparison of disease and drug profiles using Gene set Enrichment Analysis
DSS Hao Wu Dispersion shrinakge for sequencing data.
DTA Bjoern Schwalb Dynamic Transcriptome Analysis
dualKS Eric J. Kort, Yarong Yang 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
EasyqpcR Le Pape Sylvain EasyqpcR for low-throughput real-time quantitative PCR data analysis
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 Oles Image processing toolbox for R
EBSeq Ning Leng 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
EDDA Chia Kuan Hui Burton, Niranjan Nagarajan Experimental Design in Differential Abundance analysis
edgeR Yunshun Chen, Mark Robinson, Davis McCarthy, Gordon Smyth Empirical analysis of digital gene expression data in R
eiR Kevin Horan Accelerated similarity searching of small molecules
eisa Gabor Csardi Expression data analysis via the Iterative Signature Algorithm
ELBOW Graham Alvare, Xiangli Zhang ELBOW - Evaluating foLd change By the lOgit Way
ensemblVEP Valerie Obenchain R Interface to Ensembl Variant Effect Predictor
ENVISIONQuery Alex Lisovich, Roger Day Retrieval from the ENVISION bioinformatics data portal into R
epigenomix Hans-Ulrich Klein Epigenetic and gene transcription data normalization and integration with mixture models
epivizr Hector Corrada Bravo R Interface to epiviz web app
ExiMiR Sylvain Gubian R functions for the normalization of Exiqon miRNA array data
exomeCopy Michael Love Copy number variant detection from exome sequencing read depth
exomePeak Jia Meng exomePeak
explorase Michael Lawrence GUI for exploratory data analysis of systems biology data
ExpressionView Gabor Csardi Visualize biclusters identified in gene expression data
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
fastLiquidAssociation Tina Gunderson functions for genome-wide application of Liquid Association
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
FGNet Sara Aibar Functional gene networks derived from biological enrichment analyses
flagme Mark Robinson, Riccardo Romoli Analysis of Metabolomics GC/MS Data
flipflop Elsa Bernard Fast lasso-based isoform prediction as a flow problem
flowBeads Nikolas Pontikos flowBeads: Analysis of flow bead data
flowBin Kieran O'Neill Combining multitube flow cytometry data by binning
flowCL Justin Meskas flowCL: Semantic labelling of flow cytometric cell populations
flowClust Greg Finak, Mike Jiang Clustering for Flow Cytometry
flowCore M.Jiang flowCore: Basic structures for flow cytometry data
flowCyBar Joachim Schumann Analyze flow cytometric data using gate information
flowFit Davide Rambaldi Estimate proliferation in cell-tracking dye studies
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
flowMap Chiaowen Joyce Hsiao Mapping cell populations in flow cytometry data for cross-sample comparisons using the Friedman-Rafsky Test
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
flowPhyto Chris Berthiaume 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
flowQB Faysal El Khettabi Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q, B and CVinstrinsic calculations.
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 Josef Spidlen Utilities for flow cytometry
flowViz Mike Jiang Visualization for flow cytometry
flowWorkspace Greg Finak,Mike Jiang Import flowJo Workspaces into BioConductor and replicate flowJo gating with flowCore
fmcsR ChemmineR Team Mismatch Tolerant Maximum Common Substructure Searching
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
FunciSNP Simon G. Coetzee Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs
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.
gaucho Alex Murison, Christopher Wardell Genetic Algorithms for Understanding Clonal Heterogeneity and Ordering
gCMAP Thomas Sandmann Tools for Connectivity Map-like analyses
gCMAPWeb Thomas Sandmann A web interface for gene-set enrichment analyses
gcrma Z. Wu Background Adjustment Using Sequence Information
genArise IFC Development Team Microarray Analysis tool
GENE.E Joshua Gould Interact with GENE-E from R
GeneAnswers Gang Feng, Pan Du and Tian Xia Integrated Interpretation of Genes
GeneExpressionSignature Yang Cao, Fei Li,Lu Han 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
GeneMeta Bioconductor Package Maintainer MetaAnalysis for High Throughput Experiments
GeneNetworkBuilder Jianhong Ou Build Regulatory Network from ChIP-chip/ChIP-seq and Expression Data
GeneOverlap Li Shen, Mount Sinai Test and visualize gene overlaps
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
GeneSelector Martin Slawski Stability and Aggregation of ranked gene lists
geNetClassifier Sara Aibar classify diseases and build associated gene networks using gene expression profiles
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
GenomeInfoDb Bioconductor Package Maintainer Utilities for manipulating chromosome and other 'seqname' identifiers
genomeIntervals Julien Gagneur Operations on genomic intervals
genomes Chris Stubben Genome sequencing project metadata
GenomicAlignments Bioconductor Package Maintainer Representation and manipulation of short genomic alignments
GenomicFeatures Bioconductor Package Maintainer Tools for making and manipulating transcript centric annotations
GenomicFiles Bioconductor Package Maintainer Parallel queries distributed by file or by range
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 Visualization tools 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
gmapR Michael Lawrence Provides convenience methods to work with GMAP and GSNAP from within R
GOFunction Jing Wang 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 Nadia Davidson Gene Ontology analyser for RNA-seq and other length biased data
GOSim Holger Froehlich Computation of functional similarities between GO terms and gene products; GO enrichment analysis
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
gpls Bioconductor Package Maintainer Classification using generalized partial least squares
gprege Alfredo Kalaitzis Gaussian Process Ranking and Estimation of Gene Expression time-series
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
GSCA Zhicheng Ji GSCA: Gene Set Context Analysis
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 for microarray and RNA-seq data
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, Adrienne Stilp Tools for Genome Wide Association Studies
h5vc Paul Theodor Pyl Managing alignment tallies using a hdf5 backend
hapFabia Sepp Hochreiter hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data
Harshlight Maurizio Pellegrino A "corrective make-up" program for microarray chips
HCsnip Askar Obulkasim Semi-supervised adaptive-height snipping of the Hierarchical Clustering tree
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 Nicolas Servant High Throughput Chromosome Conformation Capture analysis
HMMcopy Daniel Lai, Gavin Ha, Sohrab Shah Copy number prediction with correction for GC and mappability bias for HTS data
hopach Katherine S. Pollard Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
hpar Laurent Gatto Human Protein Atlas in R
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
HTSeqGenie Jens Reeder A NGS analysis pipeline.
htSeqTools Oscar Reina Quality Control, Visualization and Processing for High-Throughput Sequencing data
HTSFilter Andrea Rau Filter replicated high-throughput transcriptome 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
iBMQ Greg Imholte integrated Bayesian Modeling of eQTL data
Icens Bioconductor Package Maintainer NPMLE for Censored and Truncated 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
idiogram Karl J. Dykema idiogram
IdMappingAnalysis Alex Lisovich, Roger Day ID Mapping Analysis
IdMappingRetrieval Alex Lisovich, Roger Day ID Mapping Data Retrieval
illuminaio Kasper Daniel Hansen Parsing Illumina microarray output files
imageHTS Joseph Barry Analysis of high-throughput microscopy-based screens
impute Balasubramanian Narasimhan impute: Imputation for microarray data
INPower Bill Wheeler An R package for computing the number of susceptibility SNPs
inSilicoDb Quentin De Clerck, David Steenhoff Access to the InSilico Database
inSilicoMerging Quentin De Clerck, David Steenhoff Collection of Merging Techniques for Gene Expression Data
intansv Wen Yao Integrative analysis of structural variations
interactiveDisplay Shawn Balcome Package for enabling powerful shiny web displays of Bioconductor objects
inveRsion Alejandro Caceres Inversions in genotype data
iontree Mingshu Cao Data management and analysis of ion trees from ion-trap mass spectrometry
iPAC Gregory Ryslik Identification of Protein Amino acid Clustering
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
jmosaics Xin Zeng Joint analysis of multiple ChIP-Seq data sets
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
KEGGprofile Shilin Zhao An annotation and visualization package for multi-types and multi-groups expression data in KEGG pathway
KEGGREST Bioconductor Package Maintainer Client-side REST access to 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
lmdme Cristobal Fresno Linear Model decomposition for Designed Multivariate Experiments
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.
lpNet Bettina Knapp Linear Programming Model for Network Inference
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
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 Chris Berthiaume, Adrian Marchetti Microbial Assemblage Normalized Transcript Analysis
MantelCorr Brian Steinmeyer Compute Mantel Cluster Correlations
maPredictDSC Adi Laurentiu Tarca Phenotype prediction using microarray data: approach of the best overall team in the IMPROVER Diagnostic Signature Challenge
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
massiR Sam Buckberry massiR: MicroArray Sample Sex Identifier
MassSpecWavelet Pan Du Mass spectrum processing by wavelet-based algorithms
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.
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 (MeD)IP-seq data analysis
MEDME Mattia Pelizzola Modelling Experimental Data from MeDIP Enrichment
MergeMaid Xiaogang Zhong Merge Maid
MeSHDbi Koki Tsuyuzaki DBI to construct MeSH-related package from sqlite file.
meshr Koki Tsuyuzaki Tools for conducting enrichment analysis of MeSH
messina Mark Pinese Single-gene classifiers and outlier-resistant detection of differential expression for two-group and survival problems.
metaArray Hyungwon Choi Integration of Microarray Data for Meta-analysis
metagenomeSeq Joseph N. Paulson Statistical analysis for sparse high-throughput sequencing
metahdep John R. Stevens Hierarchical Dependence in Meta-Analysis
metaMS Ron Wehrens MS-based metabolomics annotation pipeline
metaSeq Koki Tsuyuzaki Meta-analysis of RNA-Seq count data in multiple studies
metaseqR Panagiotis Moulos metaseqR: an R package for the analysis and result reporting of RNA-Seq gene expression data using multiple statistical algorithms.
methVisual Arie Zackay Methods for visualization and statistics on DNA methylation data
methyAnalysis Pan Du DNA methylation data analysis and visualization
methylMnM Yan Zhou detect different methylation level (DMR)
MethylSeekR Lukas Burger Segmentation of Bis-seq 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
MIMOSA Greg Finak Mixture Models for Single-Cell Assays
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's 450k methylation arrays
MinimumDistance Robert B Scharpf A package for de novo CNV detection in case-parent trios
MiPP Sukwoo Kim Misclassification Penalized Posterior Classification
MiRaGE Y-h. Taguchi MiRNA Ranking by Gene Expression
miRNApath James M. Ward miRNApath: Pathway Enrichment for miRNA Expression Data
Mirsynergy Yue Li Mirsynergy
mitoODE Gregoire Pau Implementation of the differential equation model described in "Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay"
MLInterfaces V. Carey Uniform interfaces to R machine learning procedures for data in Bioconductor containers
MLP Tobias Verbeke MLP
MLSeq Gokmen Zararsiz Machine learning interface for RNA-Seq data
MMDiff Gabriele Schweikert Statistical Testing for ChIP-Seq data sets
mmnet Yang Cao, Fei Li A metagenomic pipeline for systems biology
MmPalateMiRNA Guy Brock Murine Palate miRNA Expression Analysis
mosaics Dongjun Chung MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)
MotifDb Paul Shannon An Annotated Collection of Protein-DNA Binding Sequence Motifs
motifRG Zizhen Yao A package for discriminative motif discovery, designed for high throughput sequencing dataset
motifStack Jianhong Ou Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
MotIV Eloi Mercier, Raphael Gottardo Motif Identification and Validation
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 MSnbase: Base Functions and Classes for MS-based Proteomics
MSstats Meena Choi Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments
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
mzID Thomas Lin Pedersen An mzIdentML parser for R
mzR Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)
NarrowPeaks Pedro Madrigal Analysis of Variation in ChIP-seq using Functional PCA
ncdfFlow Mike Jiang ncdfFlow: A package that provides ncdf based storage for flow cytometry data.
NCIgraph Laurent Jacob Pathways from the NCI Pathways Database
neaGUI Setia Pramana An R package to perform the network enrichment analysis (NEA).
nem Holger Froehlich (Dynamic) Nested Effects Models and Deterministic Effects Propagation Networks to reconstruct phenotypic hierarchies
NetPathMiner Ahmed Mohamed NetPathMiner for Biological Network Construction, Path Mining and Visualization
netresponse Leo Lahti netresponse: functional network analysis
NetSAM Bing Zhang Network Seriation And Modularization
networkBMA Ka Yee Yeung Regression-based network inference using Bayesian Model Averaging
nnNorm Adi Laurentiu Tarca Spatial and intensity based normalization of cDNA microarray data based on robust neural nets
NOISeq Sonia Tarazona Exploratory analysis and differential expression for RNA-seq data
nondetects Matthew N. McCall Non-detects in qPCR data
NormqPCR James Perkins Functions for normalisation of RT-qPCR data
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
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
omicade4 Chen Meng Multiple co-inertia analysis of omics datasets
OmicCircos Ying Hu High-quality circular visualization of omic data
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
openCyto Mike Jiang Hierarchical Gating Pipeline for flow cytometry data
OrderedList Claudio Lottaz Similarities of Ordered Gene Lists
OrganismDbi Biocore Data Team Software to enable the smooth interfacing of different database packages.
OSAT Li Yan OSAT: Optimal Sample Assignment Tool
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
PADOG Adi Laurentiu Tarca Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)
paircompviz Michal Burda Multiple comparison test visualization
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
PAPi Raphael Aggio Predict metabolic pathway activity based on metabolomics data
parody VJ Carey Parametric And Resistant Outlier DYtection
pathifier Assif Yitzhaky Quantify deregulation of pathways in cancer
PathNet Jason B. Smith An R package for pathway analysis using topological information
pathRender Li Long Render molecular pathways
pathview Weijun Luo a tool set for pathway based data integration and visualization
pcaGoPromoter Morten Hansen pcaGoPromoter is used to analyze DNA micro array data
pcaMethods Henning Redestig 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
PECA Tomi Suomi Probe-level Expression Change Averaging
PGSEA Karl Dykema Parametric Gene Set Enrichment Analysis
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.
PhenStat Natasha Karp Statistical analysis of phenotypic data
phyloseq Paul J. McMurdie Handling and analysis of high-throughput microbiome census data.
piano Leif Varemo 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
PING Renan Sauteraud 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
plethy Daniel Bottomly R framework for exploration and analysis of respirometry data
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
plrs Gwenael G.R. Leday to Piecewise Linear Regression Splines (PLRS) for the association between DNA copy number and gene expression
plw Magnus Astrand Probe level Locally moderated Weighted t-tests.
ppiStats Bioconductor Package Maintainer Protein-Protein Interaction Statistical Package
prada Florian Hahne Data analysis for cell-based functional assays
prebs Karolis Uziela Probe region expression estimation for RNA-seq data for improved microarray comparability
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
ProCoNA David L Gibbs Protein co-expression network analysis (ProCoNA).
pRoloc Laurent Gatto A unifying bioinformatics framework for spatial proteomics
PROMISE Stan Pounds, Xueyuan Cao PRojection Onto the Most Interesting Statistical Evidence
prot2D Sebastien Artigaud Statistical Tools for volume data from 2D Gel Electrophoresis
proteinProfiles Julian Gehring Protein Profiling
PSICQUIC Paul Shannon Protemics Standard Initiative Common QUery InterfaCe
puma Richard Pearson Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)
pvac Jun Lu, Pierre R. Bushel PCA-based gene filtering for Affymetrix arrays
pvca Jianying LI Principal Variance Component Analysis (PVCA)
PWMEnrich Robert Stojnic PWM enrichment analysis
qcmetrics Laurent Gatto A Framework for Quality Control
QDNAseq Ilari Scheinin Quantitative DNA sequencing for chromosomal aberrations
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 Quality Control of Gated Flow Cytometry Experiments
quantsmooth Jan Oosting Quantile smoothing and genomic visualization of array data
QuasR Michael Stadler Quantify and Annotate Short Reads in R
qusage Christopher Bolen qusage: Quantitative Set Analysis for Gene Expression
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
Rariant Julian Gehring Identification and Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies
RbcBook1 Vince Carey Support for Springer monograph on Bioconductor
RBGL Bioconductor Package Maintainer An interface to the BOOST graph library
RBioinf Robert Gentleman RBioinf
rBiopaxParser Frank Kramer Parses BioPax files and represents them in R
Rbowtie Michael Stadler R bowtie wrapper
rbsurv Soo-heang Eo Robust likelihood-based survival modeling with microarray data
Rcade Jonathan Cairns R-based analysis of ChIP-seq And Differential Expression - a tool for integrating a count-based ChIP-seq analysis with differential expression summary data.
RCASPAR Douaa Mugahid, Lars Kaderali A package for survival time prediction based on a piecewise baseline hazard Cox regression model.
Rchemcpp Guenter Klambauer Similarity measures for chemical compounds
RchyOptimyx Adrin Jalali, Nima Aghaeepour Optimyzed Cellular Hierarchies for Flow Cytometry
Rcpi Nan Xiao Toolkit for Compound-Protein Interaction in Drug Discovery
RCytoscape Paul Shannon Display and manipulate graphs in Cytoscape
RDAVIDWebService Cristobal Fresno An R Package for retrieving data from DAVID into R objects using Web Services API.
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 Interactive visualization and manipulation of nested networks
REDseq Lihua Julie Zhu Analysis of high-throughput sequencing data processed by restriction enzyme digestion
RefNet Paul Shannon A queryable collection of molecular interactions, from many sources
RefPlus Kai-Ming Chang A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods.
Repitools Mark Robinson Epigenomic tools
ReportingTools Jason A. Hackney, Gabriel Becker, Jessica L. Larson Tools for making reports in various formats
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.
rfPred Hugo Varet Assign rfPred functional prediction scores to a missense variants list
rGADEM Arnaud Droit de novo motif discovery
RGalaxy Bioconductor Package Maintainer Make an R function available in the Galaxy web platform
Rgraphviz Kasper Daniel 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
RIPSeeker Yue Li RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments
Risa Alejandra Gonzalez-Beltran, ISA Team Converting experimental metadata from ISA-tab into Bioconductor data structures
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
RMassBank RMassBank at Eawag Workflow to process tandem MS files and build MassBank records
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
RNASeqPower Terry M Therneau Sample size for RNAseq studies
roar Elena Grassi Identify differential APA usage from RNA-seq alignments
ROC Vince Carey utilities for ROC, with uarray focus
Roleswitch Yue Li Infer miRNA-mRNA interactions using paired expression data from a single sample
Rolexa Jacques Rougemont Statistical analysis of Solexa sequencing data
rols Laurent Gatto An R interface to the Ontology Lookup Service
ROntoTools Calin Voichita R Onto-Tools suite
RPA Leo Lahti RPA: Robust Probabilistic Averaging for probe-level analysis
RpsiXML Jitao David Zhang R interface to PSI-MI 2.5 files
rpx Laurent Gatto R Interface to the ProteomeXchange Repository
rqubic Jitao David Zhang Qualitative biclustering algorithm for expression data analysis in R
RRHO Jonathan Rosenblatt Inference on agreement between two lists
Rsamtools Bioconductor Package Maintainer Binary alignment (BAM), variant call (BCF), or tabix file import
rsbml Michael Lawrence R support for SBML, using libsbml
rSFFreader Matt Settles rSFFreader reads in sff files generated by Roche 454 and Life Sciences Ion Torrent sequencers
Rsubread Wei Shi Rsubread package: high-performance read alignment, quantification and mutation discovery
RSVSim Christoph Bartenhagen RSVSim: an R/Bioconductor package for the simulation of structural variations
rTANDEM Frederic Fournier Interfaces the tandem protein identification algorithm in R
RTCA Jitao David Zhang Open-source toolkit to analyse data from xCELLigence System (RTCA)
RTN Mauro Castro Reconstruction of transcriptional networks and analysis of master regulators
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.
rTRM Diego Diez Identification of transcriptional regulatory modules from PPI networks
rTRMui Diego Diez A shiny user interface for rTRM
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.
sangerseqR Jonathon Hill Tools for Sanger Sequencing Data in R
SANTA Alex Cornish Spatial Analysis of Network Associations
sapFinder Shaohang Xu, Bo Wen A package for variant peptides detection and visualization in shotgun proteomics.
savR R. Brent Calder Parse and analyze Illumina SAV files
SBMLR Tomas Radivoyevitch SBML-R Interface and Analysis Tools
SCAN.UPC Stephen R. Piccolo Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
ScISI Tony Chiang In Silico Interactome
scsR Andrea Franceschini, Roger Meier, Christian von Mering SiRNA correction for seed mediated off-target effect
segmentSeq Thomas J. Hardcastle Methods for identifying small RNA loci from high-throughput sequencing data
SeqArray Xiuwen Zheng Big Data Management of Genome-wide Sequencing Variants
seqbias Daniel Jones Estimation of per-position bias in high-throughput sequencing data
seqCNA David Mosen-Ansorena Copy number analysis of high-throughput sequencing cancer data
SeqGSEA Xi Wang Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
seqLogo Oliver Bembom Sequence logos for DNA sequence alignments
SeqVarTools Stephanie M. Gogarten, Xiuwen Zheng Tools for variant data
shinyTANDEM Frederic Fournier Provides a GUI for rTANDEM
ShortRead Bioconductor Package Maintainer FASTQ input and manipulation
sigaR Wessel N. van Wieringen statistics for integrative genomics analyses in R
SigFuge Patrick Kimes SigFuge
siggenes Holger Schwender Multiple testing using SAM and Efron's empirical Bayes approaches
sigPathway Weil Lai Pathway Analysis
SIM Renee X. de Menezes Integrated Analysis on two human genomic datasets
SimBindProfiles Bettina Fischer Similar Binding Profiles
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
SNAGEE David Venet Signal-to-Noise applied to Gene Expression Experiments
snapCGH John Marioni Segmentation, normalisation and processing of aCGH data.
snm John D. Storey Supervised Normalization of Microarrays
SNPchip Robert Scharpf Visualizations for copy number alterations
snpStats David Clayton SnpMatrix and XSnpMatrix classes and methods
SomatiCA Mengjie Chen SomatiCA: identifying, characterizing, and quantifying somatic copy number aberrations from cancer genome sequencing
SomaticSignatures Julian Gehring Somatic Signatures
SpacePAC Gregory Ryslik Identification of Mutational Clusters in 3D Protein Space via Simulation.
spade Zach Bjornson SPADE -- An analysis and visualization tool for Flow Cytometry
SpeCond Florence Cavalli Condition specific detection from expression data
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
spikeLI Enrico Carlon Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool
spkTools Matthew N McCall Methods for Spike-in Arrays
splicegear Laurent Gautier splicegear
spliceR Johannes Waage, Kristoffer Vitting-Seerup Classification of alternative splicing and prediction of coding potential from RNA-seq data.
spliceSites Wolfgang Kaisers Manages align gap positions from RNA-seq data
SplicingGraphs H. Pages Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
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
sRAP Charles Warden Simplified RNA-Seq Analysis Pipeline
sscore Richard Kennedy S-Score Algorithm for Affymetrix Oligonucleotide Microarrays
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
SSPA Maarten van Iterson General Sample Size and Power Analysis for Microarray and Next-Generation Sequencing Data
staRank Juliane Siebourg Stability Ranking
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 High-dimensional Data Sets
Streamer Martin Morgan Enabling stream processing of large files
STRINGdb Andrea Franceschini, Alexander Roth, Christian Von Mering, Michael Kuhn, Lars J Jensen STRINGdb (Search Tool for the Retrieval of Interacting proteins database)
supraHex Hai Fang A supra-hexagonal map for analysing tabular omics data
survcomp Benjamin Haibe-Kains, Markus Schroeder, Catharina Olsen Performance Assessment and Comparison for Survival Analysis
Sushi Douglas H Phanstiel Tools for visualizing genomics data
sva Jeffrey T. Leek Surrogate Variable Analysis
SwimR Randy Blakely SwimR: A Suite of Analytical Tools for Quantification of C. elegans Swimming Behavior
synapter Laurent Gatto Label-free data analysis pipeline for optimal identification and quantitation
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.
TCC Jianqiang Sun, Tomoaki Nishiyama TCC: Differential expression analysis for tag count data with robust normalization strategies
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
TFBSTools Ge Tan Software package for transcription factor binding site (TFBS) analysis
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
TitanCNA Gavin Ha, Sohrab P Shah Subclonal copy number and LOH prediction whole genome sequencing of tumours
tkWidgets J. Zhang R based tk widgets
topGO Adrian Alexa topGO: Enrichment analysis for Gene Ontology
trackViewer Jianhong Ou light package to plot elegant track layers
tRanslatome Toma Tebaldi, Erik Dassi Comparison between multiple levels of gene expression.
TransView Julius Muller Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets.
triform Tony Handstad Developer Triform finds enriched regions (peaks) in transcription factor ChIP-sequencing data
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
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
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 Marc Carlson R Interface to UniProt Web Services
VanillaICE Robert Scharpf A Hidden Markov Model for high throughput genotyping arrays
VariantAnnotation Valerie Obenchain Annotation of Genetic Variants
VariantFiltering Robert Castelo Filtering of coding and non-coding genetic variants
VariantTools Michael Lawrence Tools for Working with 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
viper Mariano J Alvarez Virtual Inference of Protein-activity by Enriched Regulon analysis
virtualArray Andreas Heider Build virtual array from different microarray platforms
vsn Wolfgang Huber Variance stabilization and calibration for microarray data
vtpnet VJ Carey variant-transcription factor-phenotype networks
wateRmelon Leo Illumina 450 methylation array normalization and metrics
waveTiling Kristof De Beuf Wavelet-Based Models for Tiling Array Transcriptome Analysis
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
xps Christian Stratowa Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays
XVector H. Pages Representation and manpulation of external sequences
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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