Bioconductor Software Packages

Bioconductor version: 3.2

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
ABAEnrichment Steffi Grote Gene expression enrichment in human brain regions
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 modelling absolute expression differences
acde Juan Pablo Acosta Artificial Components Detection of Differentially Expressed Genes
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 Yifang Hu, Keith Satterley GUI for limma package with Affymetrix microarrays
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
AIMS Eric R Paquet AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype
ALDEx2 Greg Gloor Analysis of differential abundance taking sample variation into account
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
AnalysisPageServer Brad Friedman A framework for sharing interactive data and plots from R through the web.
annaffy Colin A. Smith Annotation tools for Affymetrix biological metadata
annmap Chris Wirth Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.
annotate Bioconductor Package Maintainer Annotation for microarrays
AnnotationDbi Bioconductor Package Maintainer Annotation Database Interface
AnnotationForge Bioconductor Package Maintainer Code for Building Annotation Database Packages
AnnotationFuncs Stefan McKinnon Edwards Annotation translation functions
AnnotationHub Bioconductor Package Maintainer Client to access AnnotationHub resources
AnnotationHubData Bioconductor Package Maintainer Transform public data resources into Bioconductor Data Structures
annotationTools Alexandre Kuhn Annotate microarrays and perform cross-species gene expression analyses using flat file databases.
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 Ugis Sarkans 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 report for 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
ASGSCA Hela Romdhani Association Studies for multiple SNPs and multiple traits using Generalized Structured Equation Models
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
ballgown Alyssa Frazee Flexible, isoform-level differential expression analysis
bamsignals Alessandro Mammana Extract read count signals from bam files
BaseSpaceR Jared O'Connell 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
BBCAnalyzer Sarah Sandmann BBCAnalyzer: an R/Bioconductor package for visualizing base counts
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
BEclear Markus Merl Correct for batch effects in DNA methylation 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
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 Cross-target analysis of small molecule bioactivity
Biobase Bioconductor Package Maintainer Biobase: Base functions for Bioconductor
biobroom John D. Storey and Andrew J. Bass Turn Bioconductor objects into tidy data frames
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, CRAN, and github 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), undirected and directed signed graph preserving degree distribution (or marginal totals)
birta Benedikt Zacher, Holger Froehlich Bayesian Inference of Regulation of Transcriptional Activity
birte Holger Froehlich Bayesian Inference of Regulatory Influence on Expression (biRte)
BiSeq Katja Hebestreit Processing and analyzing bisulfite sequencing data
BitSeq Antti Honkela, Panagiotis Papastamoulis Transcript expression inference and differential expression analysis for RNA-seq data
blima Vojtech Kulvait Package for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level.
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
BridgeDbR Anwesha Bohler Code for using BridgeDb identifier mapping framework from within R
BrowserViz Paul Shannon BrowserViz: interactive R/browser graphics using websockets and JSON
BrowserVizDemo Paul Shannon BrowserVizDemo: How to subclass BrowserViz
BSgenome H. Pages Infrastructure for Biostrings-based genome data packages and support for efficient SNP representation
bsseq Kasper Daniel Hansen Analyze, manage and store bisulfite sequencing data
BubbleTree Wei Zhu BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation 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 Steffen Neumann Collection of annotation related methods for mass spectrometry data
canceR Karim Mezhoud A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC.
cancerclass Daniel Kosztyla Development and validation of diagnostic tests from high-dimensional molecular data
CancerMutationAnalysis Simina M. Boca Cancer mutation analysis
CAnD Caitlin McHugh Perform Chromosomal Ancestry Differences (CAnD) Analyses
caOmicsV Henry Zhang Visualization of multi-dimentional cancer genomics data
Cardinal Kyle D. Bemis A mass spectrometry imaging toolbox for statistical 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
CausalR Glyn Bradley, Steven Barrett, Bhushan Bonde Causal Reasoning Methods
ccrepe Emma Schwager,Craig Bielski, George Weingart ccrepe_and_nc.score
cellGrowth Julien Gagneur Fitting cell population growth models
cellHTS Andrzej Oleś 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
CFAssay Herbert Braselmann Statistical analysis for the Colony Formation Assay
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 Thomas Girke R interface to a subset of OpenBabel functionalities
ChemmineR Thomas Girke Cheminformatics Toolkit for R
chimera Raffaele A Calogero A package for secondary analysis of fusion products
ChIPComp Li Chen Quantitative comparison of multiple ChIP-seq datasets
chipenrich Raymond G. Cavalcante, Chee Lee Gene Set Enrichment For ChIP-seq Peak Data
ChIPpeakAnno Lihua Julie Zhu, Jianhong Ou 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
chromDraw Jan Janecka chromDraw an R package for visualization of linear and circular karyotypes.
ChromHeatMap Tim F. Rayner Heat map plotting by genome coordinate
cisPath Likun Wang Visualization and management of the protein-protein interaction networks.
ClassifyR Dario Strbenac A framework for two-class classification problems, with applications to differential variability and differential distribution testing
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
CNPBayes Jacob Carey Bayesian mixture models for copy number polymorphisms
CNTools J. Zhang Convert segment data into a region by sample matrix to allow for other high level computational analyses.
cnvGSA Joseph Lugo Gene Set Analysis of (Rare) Copy Number Variants
CNVPanelizer Thomas Wolf Reliable CNV detection in targeted sequencing applications
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
CODEX Yuchao Jiang A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing
CoGAPS Elana J. Fertig Coordinated Gene Activity in Pattern Sets
cogena Zhilong Jia co-expressed gene-set enrichment analysis
coGPS Yingying Wei cancer outlier Gene Profile Sets
COHCAP Charles Warden CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data
coMET Tiphaine Martin coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns.
COMPASS Greg Finak Combinatorial Polyfunctionality Analysis of Single Cells
compcodeR Charlotte Soneson RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods
compEpiTools Kamal Kishore Tools for computational epigenomics
CompGO Ashley J. Waardenberg An R pipeline for .bed file annotation, comparing GO term enrichment between gene sets and data visualisation
ComplexHeatmap Zuguang Gu Making Complex Heatmaps
ConsensusClusterPlus Matt Wilkerson ConsensusClusterPlus
conumee Volker Hovestadt Enhanced copy-number variation analysis using Illumina 450k methylation arrays
convert Yee Hwa (Jean) Yang Convert Microarray Data Objects
copa James W. MacDonald Functions to perform cancer outlier profile analysis.
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
CopywriteR Thomas Kuilman Copy number information from targeted sequencing using off-target reads
CoRegNet Remy Nicolle CoRegNet : reconstruction and integrated analysis of co-regulatory networks
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.
cosmiq David Fischer, Christian Panse cosmiq - COmbining Single Masses Into Quantities
COSNet Marco Frasca Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings
CoverageView Ernesto Lowy Coverage visualization package for R
cpvSNP Caitlin McHugh Gene set analysis methods for SNP association p-values that lie in genes in given gene sets
cqn Kasper Daniel Hansen Conditional quantile normalization
CRImage Henrik Failmezger, Yinyin Yuan CRImage a package to classify cells and calculate tumour cellularity
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
csaw Aaron Lun ChIP-seq analysis with windows
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
cytofkit Jinmiao Chen, Hao Chen cytofkit: an integrated analysis pipeline for mass cytometry data
dagLogo Jianhong Ou dagLogo
daMA Jobst Landgrebe Efficient design and analysis of factorial two-colour microarray data
DAPAR Samuel Wieczorek Tools for the Differential Analysis of Proteins Abundance with R
DART Charles Shijie Zheng Denoising Algorithm based on Relevance network Topology
DASiR Ricard Illa 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
DChIPRep Bernd Klaus DChIPRep - Analysis of chromatin modification ChIP-Seq data with replication
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 data.
DEGraph Laurent Jacob Two-sample tests on a graph
DEGreport Lorena Pantano Report of DEG analysis
DEGseq Likun Wang Identify Differentially Expressed Genes from RNA-seq data
deltaGseg Diana Low deltaGseg
DeMAND Jung Hoon Woo DeMAND
derfinder Leonardo Collado-Torres Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
derfinderHelper Leonardo Collado-Torres derfinder helper package
derfinderPlot Leonardo Collado-Torres Plotting functions for derfinder
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
destiny Philipp Angerer Creates diffusion maps
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
diffHic Aaron Lun Differential analyis of Hi-C data
DiffLogo Hendrik Treutler DiffLogo: A comparative visualisation of sequence motifs
diggit Mariano J Alvarez Inference of Genetic Variants Driving Cellular Phenotypes
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.
DMRcaller Nicolae Radu Zabet Differentially Methylated Regions caller
DMRcate Tim Peters Methylation array and sequencing spatial analysis methods
DMRforPairs Martin Rijlaarsdam DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles
DNABarcodes Tilo Buschmann A tool for creating and analysing DNA barcodes used in Next Generation Sequencing multiplexing experiments
DNAcopy Venkatraman E. Seshan DNA copy number data analysis
domainsignatures Florian Hahne Geneset enrichment based on InterPro domain signatures
DOQTL Daniel Gatti Genotyping and QTL Mapping in DO Mice
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
DupChecker "Quanhu SHENG" a package for checking high-throughput genomic data redundancy in meta-analysis
dupRadar Sergi Sayols, Holger Klein Assessment of duplication rates in RNA-Seq datasets
dyebias Philip Lijnzaad The GASSCO method for correcting for slide-dependent gene-specific dye bias
DynDoc Bioconductor Package Maintainer Dynamic document tools
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 Oleś Image processing and analysis toolbox for R
EBSeq Ning Leng An R package for gene and isoform differential expression analysis of RNA-seq data
EBSeqHMM Ning Leng Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments
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
edge John D. Storey, Andrew J. Bass Extraction of Differential Gene Expression
edgeR Yunshun Chen, Aaron Lun, Mark Robinson, Davis McCarthy, Gordon Smyth Empirical analysis of digital gene expression data in R
eiR Thomas Girke 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
ELMER Lijing Yao Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
EMDomics Sadhika Malladi and Daniel Schmolze Earth Mover's Distance for Differential Analysis of Genomics Data
ENCODExplorer Charles Joly Beauparlant A compilation of ENCODE metadata
ENmix Zongli Xu Data preprocessing and quality control for Illumina HumanMethylation450 BeadChip
EnrichedHeatmap Zuguang Gu Making Enriched Heatmaps
EnrichmentBrowser Ludwig Geistlinger Seamless navigation through combined results of set-based and network-based enrichment analysis
ensembldb Johannes Rainer Utilities to create and use an Ensembl based annotation database
ensemblVEP Bioconductor Package Maintainer 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
erccdashboard Sarah Munro Assess Differential Gene Expression Experiments with ERCC Controls
erma VJ Carey epigenomic road map adventures
eudysbiome Xiaoyuan Zhou pseudo-cartesian plot and contingency test on 16S Microbial data
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 Lin Zhang, Lian Liu, Jia Meng exome-based anlaysis of MeRIP-Seq data: peak calling and differential analysis
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
facopy David Mosen-Ansorena Feature-based association and gene-set enrichment for copy number alteration analysis in cancer
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
fCI Shaojun Tang f-divergence Cutoff Index
fdrame Effi Kenigsberg FDR adjustments of Microarray Experiments (FDR-AME)
FEM Andrew E. Teschendorff Identification of Functional Epigenetic Modules
ffpe Levi Waldron Quality assessment and control for FFPE microarray expression data
FGNet Sara Aibar Functional Gene Networks derived from biological enrichment analyses
FindMyFriends Thomas Lin Pedersen Microbial Comparative Genomics in R
FISHalyseR Karesh Arunakirinathan, Andreas Heindl FISHalyseR a package for automated FISH quantification
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
flowcatchR Federico Marini Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells
flowCHIC Author: Joachim Schumann Analyze flow cytometric data using histogram information
flowCL Justin Meskas Semantic labelling of flow cytometric cell populations
flowClean Kipper Fletez-Brant flowClean
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
flowDensity Mehrnoush Malek Sequential Flow Cytometry Data Gating
flowFit Davide Rambaldi Estimate proliferation in cell-tracking dye studies
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
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.
FlowRepositoryR Josef Spidlen FlowRepository R Interface
FlowSOM Sofie Van Gassen Using self-organizing maps for visualization and interpretation of cytometry data
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
flowVS Ariful Azad Variance stabilization in flow cytometry (and microarrays)
flowWorkspace Greg Finak,Mike Jiang Import flowJo Workspaces into BioConductor and replicate flowJo gating with flowCore
fmcsR Thomas Girke Mismatch Tolerant Maximum Common Substructure Searching
focalCall Oscar Krijgsman Detection of focal aberrations in DNA copy number data
FourCSeq Felix A. Klein Package analyse 4C sequencing data
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
gcatest Wei Hao, John D. Storey Genotype Conditional Association TEST
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
gdsfmt Xiuwen Zheng R Interface to CoreArray Genomic Data Structure (GDS) Files
geecc Markus Boenn Gene set Enrichment analysis Extended to Contingency Cubes
genArise IFC Development Team Microarray Analysis tool
GENE.E Joshua Gould Interact with GENE-E from R
GeneAnswers Lei Huang and Gang Feng Integrated Interpretation of Genes
GeneBreak Evert van den Broek Gene Break Detection
GeneExpressionSignature Yang Cao, Fei Li,Lu Han Gene Expression Signature based Similarity Metric
genefilter Bioconductor Package Maintainer genefilter: methods for filtering genes from high-throughput experiments
genefu Benjamin Haibe-Kains, Markus Schroeder Computation of Gene Expression-Based Signatures in Breast Cancer
GeneGA Zhenpeng Li Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm
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
GENESIS Matthew P. Conomos GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
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
genomation Altuna Akalin, Vedran Franke Summary, annotation and visualization of genomic data
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 Distributed computing by file or by range
GenomicInteractions Malcolm Perry, Liz Ing-Simmons R package for handling genomic interaction data
GenomicRanges Bioconductor Package Maintainer Representation and manipulation of genomic intervals and variables defined along a genome
GenomicTuples Peter Hickey Representation and Manipulation of Genomic Tuples
Genominator James Bullard Analyze, manage and store genomic data
genoset Peter M. Haverty Provides classes similar to ExpressionSet for copy number analysis
genotypeeval Jennifer Tom QA/QC of a gVCF or VCF file
GenoView Sharon Lee Condensed, overlapped plotting of genomic data tracks
GEOmetadb Jack Zhu A compilation of metadata from NCBI GEO
GEOquery Sean Davis Get data from NCBI Gene Expression Omnibus (GEO)
GEOsearch Zhicheng Ji GEOsearch
GEOsubmission Alexandre Kuhn Prepares microarray data for submission to GEO
gespeR Fabian Schmich Gene-Specific Phenotype EstimatoR
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
ggtree Guangchuang Yu a phylogenetic tree viewer for different types of tree annotations
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 An R interface to the GMAP/GSNAP/GSTRUCT suite
GOexpress Kevin Rue-Albrecht Visualise microarray and RNAseq data using gene ontology annotations
GOFunction Jing Wang GO-function: deriving biologcially relevant functions from statistically significant functions
GoogleGenomics Siddhartha Bagaria R Client for Google Genomics API
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.
GOsummaries Raivo Kolde Word cloud summaries of GO enrichment analysis
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
gQTLBase VJ Carey gQTLBase: infrastructure for eQTL, mQTL and similar studies
gQTLstats VJ Carey gQTLstats: computationally efficient analysis for eQTL and allied studies
graph Bioconductor Package Maintainer graph: A package to handle graph data structures
GraphAlignment Joern P. Meier GraphAlignment
GraphAT Thomas LaFramboise Graph Theoretic Association Tests
graphite Gabriele Sales GRAPH Interaction from pathway Topological Environment
GraphPAC Gregory Ryslik Identification of Mutational Clusters in Proteins via a Graph Theoretical Approach.
GRENITS Edward Morrissey Gene Regulatory Network Inference Using Time Series
GreyListChIP Gordon Brown Grey Lists -- Mask Artefact Regions Based on ChIP Inputs
groHMM Anusha Nagari, W. Lee Kraus GRO-seq Analysis Pipeline.
GSAR Yasir Rahmatallah, Galina Glazko Gene Set Analysis in R
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
GSReg Bahman Afsari Gene Set Regulation (GS-Reg)
GSRI Julian Gehring Gene Set Regulation Index
GSVA Justin Guinney Gene Set Variation Analysis for microarray and RNA-seq data
gtrellis Zuguang Gu Genome Level Trellis Layout
GUIDEseq Lihua Julie Zhu GUIDE-seq analysis pipeline
Guitar Jia Meng Guitar
Gviz Florian Hahne Plotting data and annotation information along genomic coordinates
gwascat VJ Carey representing and modeling data in the EMBL-EBI 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
HDTD Anestis Touloumis Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD)
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
hiAnnotator Nirav V Malani Functions for annotating GRanges objects.
HIBAG Xiuwen Zheng HLA Genotype Imputation with Attribute Bagging
hierGWAS Laura Buzdugan Asessing statistical significance in predictive GWA studies
HilbertCurve Zuguang Gu Making 2D Hilbert Curve
HilbertVis Simon Anders Hilbert curve visualization
HilbertVisGUI Simon Anders HilbertVisGUI
hiReadsProcessor Nirav V Malani Functions to process LM-PCR reads from 454/Illumina data
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
iCheck Weiliang Qiu QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data
iChip Qianxing Mo Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models
iClusterPlus Qianxing Mo, Ronglai Shen Integrative clustering of multi-type genomic data
IdeoViz Shraddha Pai Plots data (continuous/discrete) along chromosomal ideogram
idiogram Karl J. Dykema idiogram
IdMappingAnalysis Alex Lisovich, Roger Day ID Mapping Analysis
IdMappingRetrieval Alex Lisovich, Roger Day ID Mapping Data Retrieval
iGC Liang-Bo Wang An integrated analysis package of Gene expression and Copy number alteration
illuminaio Kasper Daniel Hansen Parsing Illumina Microarray Output Files
imageHTS Joseph Barry Analysis of high-throughput microscopy-based screens
Imetagene Audrey Lemacon A graphical interface for the metagene package
immunoClust Till Soerensen immunoClust - Automated Pipeline for Population Detection in Flow Cytometry
IMPCdata Jeremy Mason Retrieves data from IMPC database
impute Balasubramanian Narasimhan impute: Imputation for microarray data
InPAS Jianhong Ou Identification of Novel alternative PolyAdenylation Sites (PAS)
INPower Bill Wheeler An R package for computing the number of susceptibility SNPs
inSilicoDb InSilico DB Access to the InSilico Database
inSilicoMerging InSilico DB Collection of Merging Techniques for Gene Expression Data
INSPEcT Stefano de Pretis Analysis of 4sU-seq and RNA-seq time-course data
intansv Wen Yao Integrative analysis of structural variations
interactiveDisplay Shawn Balcome Package for enabling powerful shiny web displays of Bioconductor objects
interactiveDisplayBase Shawn Balcome Base package for enabling powerful shiny web displays of Bioconductor objects
inveRsion Alejandro Caceres Inversions in genotype data
IONiseR Mike Smith Quality Assessment Tools for Oxford Nanopore MinION 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
iterativeBMA Ka Yee Yeung The Iterative Bayesian Model Averaging (BMA) algorithm
iterativeBMAsurv Ka Yee Yeung The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis
IVAS Seonggyun Han Identification of genetic Variants affecting Alternative Splicing
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
kebabs Ulrich Bodenhofer Kernel-Based Analysis Of Biological Sequences
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.
ldblock VJ Carey data structures for linkage disequilibrium measures in populations
LEA Eric Frichot LEA: an R package for Landscape and Ecological Association Studies
LedPred Aitor Gonzalez Learning from DNA to Predict enhancers
les Julian Gehring Identifying Differential Effects in Tiling Microarray Data
lfa Wei Hao, John D. Storey Logistic Factor Analysis for Categorical Data
limma Gordon Smyth Linear Models for Microarray Data
limmaGUI Yifang Hu, Keith Satterley GUI for limma package with two color microarrays
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
LOLA Nathan Sheffield Location overlap analysis for enrichment of genomic ranges
LowMACA Stefano de Pretis, Giorgio Melloni LowMACA - Low frequency Mutation Analysis via Consensus Alignment
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 Lars Kaderali 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
M3D Tom Mayo Identifies differentially methylated regions across testing groups
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
MAIT Francesc Fernandez-Albert Statistical Analysis of Metabolomic Data
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
mAPKL Argiris Sakellariou A Hybrid Feature Selection method for gene expression data
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.
MatrixRider Elena Grassi Obtain total affinity and occupancies for binding site matrices on a given sequence
MBAmethyl Tao Wang Model-based analysis of DNA methylation data
MBASED Oleg Mayba Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection
MBCB 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
mdgsa David Montaner Multi Dimensional Gene Set Analysis.
mdqc Gabriela Cohen-Freue Mahalanobis Distance Quality Control for microarrays
MEAL Carlos Ruiz Perform methylation analysis
MeasurementError.cor Beiying Ding Measurement Error model estimate for correlation coefficient
MEDIPS Lukas Chavez DNA IP-seq data analysis
MEDME Mattia Pelizzola Modelling Experimental Data from MeDIP Enrichment
MEIGOR Jose Egea MEIGO - MEtaheuristics for bIoinformatics Global Optimization
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
MeSHSim Jing ZHou MeSH(Medical Subject Headings) Semantic Similarity Measures
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
Metab Raphael Aggio Metab: An R Package for a High-Throughput Analysis of Metabolomics Data Generated by GC-MS.
metabomxtr Michael Nodzenski A package to run mixture models for truncated metabolomics data with normal or lognormal distributions
metagene Charles Joly Beauparlant A package to produce metagene plots
metagenomeFeatures Nathan D. Olson Exploration of marker-gene sequence taxonomic annotations
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 An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.
metaX Bo Wen An R package for metabolomic data analysis
MethTargetedNGS Muhammad Ahmer Jamil Perform Methylation Analysis on Next Generation Sequencing Data
methVisual Arie Zackay Methods for visualization and statistics on DNA methylation data
methyAnalysis Pan Du DNA methylation data analysis and visualization
MethylAid M. van Iterson Visual and interactive quality control of large Illumina 450k data sets
MethylMix Olivier Gevaert MethylMix: Identifying methylation driven cancer genes.
methylMnM Yan Zhou detect different methylation level (DMR)
methylPipe Kamal Kishore Base resolution DNA methylation data analysis
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
MGFM Khadija El Amrani Marker Gene Finder in Microarray 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
miRcomp Matthew N. McCall Tools to assess and compare miRNA expression estimatation methods
mirIntegrator Diana Diaz Integrating microRNA expression into signaling pathways for pathway analysis
miRLAB Thuc Duy Le Dry lab for exploring miRNA-mRNA relationships
miRNApath James M. Ward miRNApath: Pathway Enrichment for miRNA Expression Data
miRNAtap Maciej Pajak miRNAtap: microRNA Targets - Aggregated Predictions
Mirsynergy Yue Li Mirsynergy
missMethyl Belinda Phipson, Jovana Maksimovic Analysis of methylation array data
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
mogsa Chen Meng Multiple omics data integration and gene set analysis
monocle Cole Trapnell Analysis tools for single-cell expression experiments.
MoPS Philipp Eser MoPS - Model-based Periodicity Screening
mosaics Dongjun Chung MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)
motifbreakR Simon Gert Coetzee A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites
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
MPFE Conrad Burden Estimation of the amplicon methylation pattern distribution from bisulphite sequencing data
mQTL.NMR Lyamine Hedjazi Metabolomic Quantitative Trait Locus Mapping for 1H NMR data
msa Ulrich Bodenhofer Multiple Sequence Alignment
MSGFgui Thomas Lin Pedersen A shiny GUI for MSGFplus
MSGFplus Thomas Lin Pedersen An interface between R and MS-GF+
msmsEDA Josep Gregori Exploratory Data Analysis of LC-MS/MS data by spectral counts
msmsTests Josep Gregori i Font LC-MS/MS Differential Expression Tests
MSnbase Laurent Gatto Base Functions and Classes for MS-based Proteomics
MSnID Vlad Petyuk Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications.
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
MultiMed Simina M. Boca Testing multiple biological mediators simultaneously
multiscan Mizanur Khondoker R package for combining multiple scans
multtest Katherine S. Pollard Resampling-based multiple hypothesis testing
muscle Alex T. Kalinka Multiple Sequence Alignment with MUSCLE
MVCClass Elizabeth Whalen Model-View-Controller (MVC) Classes
mvGST John R. Stevens Multivariate and directional gene set testing
mygene Adam Mark, Chunlei Wu Access MyGene.Info_ services
myvariant Adam Mark, Chunlei Wu Accesses variant query and annotation services
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 and mzIdentML files (mass spectrometry data)
NanoStringDiff hong wang Differential Expression Analysis of NanoString nCounter Data
NanoStringQCPro Robert Ziman Quality metrics and data processing methods for NanoString mRNA gene expression data
NarrowPeaks Pedro Madrigal Shape-based Analysis of Variation in ChIP-seq using Functional PCA
ncdfFlow Mike Jiang ncdfFlow: A package that provides HDF5 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
netbenchmark Pau Bellot Benchmarking of several gene network inference methods
netbiov Shailesh tripathi A package for visualizing complex biological network
nethet Nicolas Staedler, Frank Dondelinger A bioconductor package for high-dimensional exploration of biological network heterogeneity
NetPathMiner Ahmed Mohamed NetPathMiner for Biological Network Construction, Path Mining and Visualization
netresponse Leo Lahti Functional Network Analysis
NetSAM Bing Zhang Network Seriation And Modularization
networkBMA Ka Yee Yeung Regression-based network inference using Bayesian Model Averaging
NGScopy Xiaobei Zhao NGScopy: Detection of Copy Number Variations in Next Generation Sequencing sequencing
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 Valeriia Sherina 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 Ricard Illa 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
OGSA Michael F. Ochs Outlier Gene Set Analysis
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 omics data
OmicsMarkeR Charles E. Determan Jr. Classification and Feature Selection for 'Omics' Datasets
OncoSimulR Ramon Diaz-Uriarte Forward Genetic Simulation of Cancer Progresion with Epistasis
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
OperaMate Chenglin Liu An R package of Data Importing, Processing and Analysis for Opera High Content Screening System
oposSOM Henry Loeffler-Wirth Comprehensive analysis of transciptome 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
Oscope Ning Leng Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq
OTUbase Daniel Beck Provides structure and functions for the analysis of OTU data
OutlierD Sukwoo Kim Outlier detection using quantile regression on the M-A scatterplots of high-throughput data
PAA Michael Turewicz, Martin Eisenacher PAA (Protein Array Analyzer)
PADOG Adi Laurentiu Tarca Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)
paircompviz Michal Burda Multiple comparison test visualization
pandaR Dan Schlauch PANDA algorithm
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
parglms VJ Carey support for parallelized estimation of GLMs/GEEs
parody VJ Carey Parametric And Resistant Outlier DYtection
Path2PPI Oliver Philipp Prediction of pathway-specific protein-protein interaction networks
pathifier Assif Yitzhaky Quantify deregulation of pathways in cancer
PathNet Jason B. Smith An R package for pathway analysis using topological information
pathRender Vince Carey Render molecular pathways
pathVar Samuel Zimmerman Methods to Find Pathways with Significantly Different Variability
pathview Weijun Luo a tool set for pathway based data integration and visualization
paxtoolsr Augustin Luna PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons
Pbase Sebastian Gibb, Laurent Gatto Manipulating and exploring protein and proteomics data
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
pepStat Gregory C Imholte Statistical analysis of peptide microarrays
pepXMLTab Xiaojing Wang Parsing pepXML files and filter based on peptide FDR.
PGA Bo Wen, Shaohang Xu An package for identification of novel peptides by customized database derived from RNA-Seq
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.
pmm Anna Drewek Parallel Mixed Model
podkat Ulrich Bodenhofer Position-Dependent Kernel Association Test
polyester Alyssa Frazee, Jeff Leek Simulate RNA-seq reads
Polyfit Conrad Burden Add-on to DESeq to improve p-values and q-values
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
Prize Daryanaz Dargahi Prize: an R package for prioritization estimation based on analytic hierarchy process
proBAMr Xiaojing Wang Generating SAM file for PSMs in shotgun proteomics data
PROcess Xiaochun Li Ciphergen SELDI-TOF Processing
procoil Ulrich Bodenhofer Prediction of Oligomerization of Coiled Coil Proteins
ProCoNA David L Gibbs Protein co-expression network analysis (ProCoNA).
pRoloc Laurent Gatto A unifying bioinformatics framework for spatial proteomics
pRolocGUI Laurent Gatto, Thomas Naake Interactive visualisation of spatial proteomics data
PROMISE Stan Pounds, Xueyuan Cao PRojection Onto the Most Interesting Statistical Evidence
PROPER Hao Wu PROspective Power Evaluation for RNAseq
Prostar Samuel Wieczorek Provides a GUI for DAPAR
prot2D Sebastien Artigaud Statistical Tools for volume data from 2D Gel Electrophoresis
proteinProfiles Julian Gehring Protein Profiling
ProteomicsAnnotationHubData Laurent Gatto Transform public proteomics data resources into Bioconductor Data Structures
proteoQC Bo Wen An R package for proteomics data quality control
ProtGenerics Laurent Gatto S4 generic functions for Bioconductor proteomics infrastructure
PSEA Alexandre Kuhn Population-Specific Expression Analysis.
PSICQUIC Paul Shannon Proteomics Standard Initiative Common QUery InterfaCe
puma Xuejun Liu 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)
Pviz Renan Sauteraud Peptide Annotation and Data Visualization using Gviz
PWMEnrich Robert Stojnic PWM enrichment analysis
pwOmics Astrid Wachter Pathway-based data integration of omics data
qcmetrics Laurent Gatto A Framework for Quality Control
QDNAseq Daoud Sie Quantitative DNA sequencing for chromosomal aberrations
qpcrNorm Jessica Mar Data-driven normalization strategies for high-throughput qPCR data.
qpgraph Robert Castelo Estimation of genetic and molecular regulatory networks from high-throughput genomics data
qrqc Vince Buffalo Quick Read Quality Control
QUALIFIER Mike Jiang Quality Control of Gated Flow Cytometry Experiments
quantro Stephanie Hicks A test for when to use quantile normalization
quantsmooth Jan Oosting Quantile smoothing and genomic visualization of array data
QuartPAC Gregory Ryslik Identification of mutational clusters in protein quaternary structures.
QuasR Michael Stadler Quantify and Annotate Short Reads in R
qusage Christopher Bolen qusage: Quantitative Set Analysis for Gene Expression
qvalue John D. Storey, Andrew J. Bass Q-value estimation for false discovery rate control
R3CPET Mohamed Nadhir Djekidel 3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process
r3Cseq Supat Thongjuea 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
rain Paul F. Thaben Rhythmicity Analysis Incorporating Non-parametric Methods
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
RareVariantVis Tomasz Stokowy Visualization of rare variants in whole genome sequencing data
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
RBM Dongmei Li RBM: a R package for microarray and RNA-Seq data analysis
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.
rcellminer Augustin Luna, Vinodh Rajapakse rcellminer: Molecular Profiles and Drug Response for the NCI-60 Cell Lines
rCGH Frederic Commo Comprehensive Pipeline for Analyzing and Visualizing Agilent and Affymetrix Array-Based CGH Data
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
RCy3 Tanja Muetze, Paul Shannon, Georgi Kolishovski Display and manipulate graphs in Cytoscape >= 3.2.1
RCyjs Paul Shannon Display and manipulate graphs in cytoscape.js
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.
regioneR Bernat Gel Association analysis of genomic regions based on permutation tests
regionReport Leonardo Collado-Torres Generate HTML reports for exploring a set of regions
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
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
rGREAT Zuguang Gu Client for GREAT Analysis
RGSEA Chengcheng Ma Random Gene Set Enrichment Analysis
rgsepd Karl Stamm Gene Set Enrichment / Projection Displays
rhdf5 Bernd Fischer HDF5 interface to R
Rhtslib Bioconductor Package Maintainer HTSlib high-throughput sequencing library as an R package
rHVDM Martino Barenco Hidden Variable Dynamic Modeling
RiboProfiling A. Popa Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation
riboSeqR Thomas J. Hardcastle Analysis of sequencing data from ribosome profiling experiments.
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 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
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 Lars Kaderali Statistical analysis of high-throughput RNAi screens
RNAprobR Nikos Sidiropoulos An R package for analysis of massive parallel sequencing based RNA structure probing data
rnaseqcomp Mingxiang Teng Benchmarks for RNA-seq Quantification Pipelines
rnaSeqMap Michal Okoniewski rnaSeq secondary analyses
RNASeqPower Terry M Therneau Sample size for RNAseq studies
RnaSeqSampleSize Shilin Zhao RnaSeqSampleSize
RnBeads Fabian Mueller RnBeads
Rnits Dipen P. Sangurdekar R Normalization and Inference of Time Series data
roar Elena Grassi Identify differential APA usage from RNA-seq alignments
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
ropls Etienne A. Thevenot PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data
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
Rqc Welliton Souza Quality Control Tool for High-Throughput Sequencing Data
rqubic Jitao David Zhang Qualitative biclustering algorithm for expression data analysis in R
rRDP Michael Hahsler Interface to the RDP Classifier
RRHO Jonathan Rosenblatt Inference on agreement between ordered lists
Rsamtools Bioconductor Package Maintainer Binary alignment (BAM), FASTA, variant call (BCF), and 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 Subread sequence alignment for R
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)
RTCGA Marcin Kosinski The Cancer Genome Atlas Data Integration
RTCGAToolbox Mehmet Kemal Samur A new tool for exporting TCGA Firehose data
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
RUVcorr Saskia Freytag Removal of unwanted variation for gene-gene correlations and related analysis
RUVnormalize Laurent Jacob RUV for normalization of expression array data
RUVSeq Davide Risso Remove Unwanted Variation from RNA-Seq Data
RWebServices Martin Morgan Expose R functions as web services through Java/Axis/Apache
S4Vectors Bioconductor Package Maintainer S4 implementation of vectors and lists
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 J. Cornish Spatial Analysis of Network Associations
sapFinder Shaohang Xu, Bo Wen A package for variant peptides detection and visualization in shotgun proteomics.
saps Daniel Schmolze Significance Analysis of Prognostic Signatures
savR R. Brent Calder Parse and analyze Illumina SAV files
sbgr Nan Xiao R Client for Seven Bridges Genomics API
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
SELEX Harmen Bussemaker Functions for analyzing SELEX-seq data
SemDist Ian Gonzalez Information Accretion-based Function Predictor Evaluation
SEPA Zhicheng Ji SEPA
seq2pathway Xinan Yang with contribution from Lorenzo Pesce and Ana Marija Sokovic a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data
SeqArray Xiuwen Zheng Big Data Management of Genome-Wide Sequence 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
seqPattern Vanja Haberle Visualising oligonucleotide patterns and motif occurrences across a set of sorted sequences
seqplots Przemyslaw Stempor An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps
seqTools Wolfgang Kaisers Analysis of nucleotide, sequence and quality content on fastq files.
SeqVarTools Stephanie M. Gogarten, Xiuwen Zheng, Adrienne Stilp Tools for variant data
SGSeq Leonard Goldstein Splice event prediction and quantification from RNA-seq data
shinyMethyl Jean-Philippe Fortin Interactive visualization for Illumina's 450k methylation arrays
shinyTANDEM Frederic Fournier Provides a GUI for rTANDEM
ShortRead Bioconductor Package Maintainer FASTQ input and manipulation
SICtools Xiaobin Xing Find SNV/Indel differences between two bam files with near relationship
sigaR Wessel N. van Wieringen statistics for integrative genomics analyses in R
SigCheck Rory Stark Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadata
SigFuge Patrick Kimes SigFuge
siggenes Holger Schwender Multiple testing using SAM and Efron's empirical Bayes approaches
sigPathway Weil Lai Pathway Analysis
sigsquared UnJin Lee Gene signature generation for functionally validated signaling pathways
SIM Renee X. de Menezes Integrated Analysis on two human genomic datasets
SIMAT Mo R. Nezami Ranjbar GC-SIM-MS data processing and alaysis tool
SimBindProfiles Bettina Fischer Similar Binding Profiles
similaRpeak Astrid Louise Deschenes similaRpeak: Metrics to estimate a level of similarity between two ChIP-Seq profiles
simpleaffy Crispin Miller Very simple high level analysis of Affymetrix data
simulatorZ Yuqing Zhang Simulator for Collections of Independent Genomic Data Sets
sincell Miguel Julia, Antonio Rausell R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data
SISPA Bhakti Dwivedi SISPA: Method for Sample Integrated Set Profile Analysis
sizepower Weiliang Qiu Sample Size and Power Calculation in Micorarray Studies
SJava Martin Morgan The Omegahat interface for R and Java
skewr Ryan Putney Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip
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
SNPhood Christian Arnold SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data
SNPRelate Xiuwen Zheng Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data
snpStats David Clayton SnpMatrix and XSnpMatrix classes and methods
soGGi Tom Carroll Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots Summarised Over Grouped Genomic Intervals
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
specL Christian Panse, Witold E. Wolski specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics
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 A bioconductor package for exploration of alignment 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
ssviz Diana Low A small RNA-seq visualizer and analysis toolkit
STAN Benedikt Zacher STrand-specific ANnotation of genomic data
staRank Juliane Siebourg Stability Ranking
Starr Benedikt Zacher Simple tiling array analysis of Affymetrix ChIP-chip data
STATegRa David Gomez-Cabrero, Patricia Sebastián-León, Gordon Ball Classes and methods for multi-omics data integration
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 STRINGdb (Search Tool for the Retrieval of Interacting proteins database)
subSeq Andrew J. Bass, John D. Storey Subsampling of high-throughput sequencing count data
SummarizedExperiment Bioconductor Package Maintainer SummarizedExperiment container
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, John D. Storey, W. Evan Johnson Surrogate Variable Analysis
SVM2CRM Guidantonio Malagoli Tagliazucchi SVM2CRM: support vector machine for cis-regulatory elements detections
SWATH2stats Peter Blattmann Transform and Filter SWATH Data for Statistical Packages
SwimR Randy Blakely SwimR: A Suite of Analytical Tools for Quantification of C. elegans Swimming Behavior
switchBox Bahman Afsari, Luigi Marchionni Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair (KTSP) algorithm.
synapter Laurent Gatto and Sebastian Gibb Label-free data analysis pipeline for optimal identification and quantitation
synlet Chunxuan Shao Hits Selection for Synthetic Lethal RNAi Screen Data
systemPipeR Thomas Girke systemPipeR: NGS workflow and report generation environment
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
TarSeqQC Gabriela Merino TARgeted SEQuencing Experiment Quality Control
TCC Jianqiang Sun, Tomoaki Nishiyama TCC: Differential expression analysis for tag count data with robust normalization strategies
TCGAbiolinks Antonio Colaprico, Tiago Chedraoui Silva TCGAbiolinks: An R/Bioconductor package for integrative analysis with TCGA 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
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
TIN Bjarne Johannessen Transcriptome instability analysis
TitanCNA Gavin Ha, Sohrab P Shah Subclonal copy number and LOH prediction from whole genome sequencing of tumours
tkWidgets J. Zhang R based tk widgets
ToPASeq Ivana Ihnatova Package for Topology-based Pathway Analysis of RNASeq data
topGO Adrian Alexa topGO: Enrichment analysis for Gene Ontology
TPP Dorothee Childs Analyze thermal proteome profiling (TPP) experiments
tracktables Tom Carroll Build IGV tracks and HTML reports
trackViewer Jianhong Ou A bioconductor package with minimalist design for plotting 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.
traseR li chen GWAS trait-associated SNP enrichment analyses in genomic intervals
triform Thomas Carroll 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
TRONCO BIMIB Group TRONCO, an R package for TRanslational ONCOlogy
TSCAN Zhicheng Ji TSCAN: Tools for Single-Cell ANalysis
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 Bioconductor Package Maintainer R Interface to UniProt Web Services
VanillaICE Robert Scharpf A Hidden Markov Model for high throughput genotyping arrays
variancePartition Gabriel E. Hoffman Quantifying and interpreting drivers of variation in complex gene expression studies
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
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
wavClusteR Federico Comoglio Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data
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
XBSeq Yuanhang Liu Test for differential expression for RNA-seq data
xcms Steffen Neumann LC/MS and GC/MS Data Analysis
XDE Robert Scharpf XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression
xmapbridge Chris Wirth 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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