All R packages

a4
Automated Affymetrix Array Analysis Umbrella Package
a4Base
Automated Affymetrix Array Analysis Base Package
a4Classif
Automated Affymetrix Array Analysis Classification Package
a4Core
Automated Affymetrix Array Analysis Core Package
a4Preproc
Automated Affymetrix Array Analysis Preprocessing Package
a4Reporting
Automated Affymetrix Array Analysis Reporting Package
ABAEnrichment
Gene expression enrichment in human brain regions
ABarray
Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Microrarray (AB1700) gene expression data.
ABSSeq
ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences
acde
Artificial Components Detection of Differentially Expressed Genes
aCGH
Classes and functions for Array Comparative Genomic Hybridization data.
ACME
Algorithms for Calculating Microarray Enrichment (ACME)
ADaCGH2
Analysis of big data from aCGH experiments using parallel computing and ff objects
adSplit
Annotation-Driven Clustering
affxparser
Affymetrix File Parsing SDK
affy
Methods for Affymetrix Oligonucleotide Arrays
affycomp
Graphics Toolbox for Assessment of Affymetrix Expression Measures
AffyCompatible
Affymetrix GeneChip software compatibility
affyContam
structured corruption of affymetrix cel file data
affycoretools
Functions useful for those doing repetitive analyses with Affymetrix GeneChips
AffyExpress
Affymetrix Quality Assessment and Analysis Tool
affyILM
Linear Model of background subtraction and the Langmuir isotherm
affyio
Tools for parsing Affymetrix data files
affylmGUI
GUI for limma package with Affymetrix microarrays
affyPara
Parallelized preprocessing methods for Affymetrix Oligonucleotide Arrays
affypdnn
Probe Dependent Nearest Neighbours (PDNN) for the affy package
affyPLM
Methods for fitting probe-level models
affyQCReport
QC Report Generation for affyBatch objects
AffyRNADegradation
Analyze and correct probe positional bias in microarray data due to RNA degradation
AffyTiling
Easy extraction of individual probes in Affymetrix tiling arrays
AGDEX
Agreement of Differential Expression Analysis
agilp
Agilent expression array processing package
AgiMicroRna
Processing and Differential Expression Analysis of Agilent microRNA chips
AIMS
AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype
ALDEx2
Analysis Of Differential Abundance Taking Sample Variation Into Account
AllelicImbalance
Investigates Allele Specific Expression
alpine
alpine
alsace
ALS for the Automatic Chemical Exploration of mixtures
altcdfenvs
alternative CDF environments (aka probeset mappings)
AMOUNTAIN
Active modules for multilayer weighted gene co-expression networks: a continuous optimization approach
ampliQueso
Analysis of amplicon enrichment panels
AnalysisPageServer
A framework for sharing interactive data and plots from R through the web.
anamiR
An integrated analysis package of miRNA and mRNA expression data
Anaquin
Statistical analysis of sequins
AneuFinder
Analysis of Copy Number Variation in Single-Cell-Sequencing Data
annaffy
Annotation tools for Affymetrix biological metadata
annmap
Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.
annotate
Annotation for microarrays
AnnotationDbi
Annotation Database Interface
AnnotationForge
Code for Building Annotation Database Packages
AnnotationFuncs
Annotation translation functions
AnnotationHub
Client to access AnnotationHub resources
AnnotationHubData
Transform public data resources into Bioconductor Data Structures
annotationTools
Annotate microarrays and perform cross-species gene expression analyses using flat file databases.
annotatr
Annotation of Genomic Regions to Genomic Annotations
anota
ANalysis Of Translational Activity (ANOTA).
antiProfiles
Implementation of gene expression anti-profiles
apComplex
Estimate protein complex membership using AP-MS protein data
aroma.light
Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types
ArrayExpress
Access the ArrayExpress Microarray Database at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet
ArrayExpressHTS
ArrayExpress High Throughput Sequencing Processing Pipeline
arrayMvout
multivariate outlier detection for expression array QA
arrayQuality
Assessing array quality on spotted arrays
arrayQualityMetrics
Quality metrics report for microarray data sets
ArrayTools
geneChip Analysis Package
ArrayTV
Implementation of wave correction for arrays
ARRmNormalization
Adaptive Robust Regression normalization for Illumina methylation data
ASAFE
Ancestry Specific Allele Frequency Estimation
ASEB
Predict Acetylated Lysine Sites
ASGSCA
Association Studies for multiple SNPs and multiple traits using Generalized Structured Equation Models
asmn
All sample mean normalization.
ASpli
Analysis of alternative splicing using RNA-Seq
ASSET
An R package for subset-based association analysis of heterogeneous traits and subtypes
ASSIGN
Adaptive Signature Selection and InteGratioN (ASSIGN)
AtlasRDF
Gene Expression Atlas query and gene set enrichment package.
attract
Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape
BaalChIP
BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes
BAC
Bayesian Analysis of Chip-chip experiment
bacon
Controlling bias and inflation in association studies using the empirical null distribution
BADER
Bayesian Analysis of Differential Expression in RNA Sequencing Data
BadRegionFinder
BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage
BAGS
A Bayesian Approach for Geneset Selection
ballgown
Flexible, isoform-level differential expression analysis
bamsignals
Extract read count signals from bam files
BaseSpaceR
R SDK for BaseSpace RESTful API
Basic4Cseq
Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
BasicSTARRseq
Basic peak calling on STARR-seq data
BatchQC
Batch Effects Quality Control Software
BayesKnockdown
BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data
BayesPeak
Bayesian Analysis of ChIP-seq Data
baySeq
Empirical Bayesian analysis of patterns of differential expression in count data
BBCAnalyzer
BBCAnalyzer: an R/Bioconductor package for visualizing base counts
BCRANK
Predicting binding site consensus from ranked DNA sequences
beadarray
Quality assessment and low-level analysis for Illumina BeadArray data
beadarraySNP
Normalization and reporting of Illumina SNP bead arrays
BeadDataPackR
Compression of Illumina BeadArray data
BEAT
BEAT - BS-Seq Epimutation Analysis Toolkit
BEclear
Correct for batch effects in DNA methylation data
betr
Identify differentially expressed genes in microarray time-course data
bgafun
BGAfun A method to identify specifity determining residues in protein families
BgeeDB
Annotation and gene expression data retrieval from Bgee database
BGmix
Bayesian models for differential gene expression
bgx
Bayesian Gene eXpression
BHC
Bayesian Hierarchical Clustering
BicARE
Biclustering Analysis and Results Exploration
BiGGR
Constraint based modeling in R using metabolic reconstruction databases
bigmelon
Illumina methylation array analysis for large experiments
bigmemoryExtras
An extension of the bigmemory package with added safety, convenience, and a factor class
bioassayR
Cross-target analysis of small molecule bioactivity
Biobase
Biobase: Base functions for Bioconductor
biobroom
Turn Bioconductor objects into tidy data frames
bioCancer
Interactive Multi-Omics Cancers Data Visualization and Analysis
BiocCaseStudies
BiocCaseStudies: Support for the Case Studies Monograph
BiocCheck
Bioconductor-specific package checks
BiocGenerics
S4 generic functions for Bioconductor
biocGraph
Graph examples and use cases in Bioinformatics
BiocInstaller
Install/Update Bioconductor, CRAN, and github Packages
BiocParallel
Bioconductor facilities for parallel evaluation
BiocStyle
Standard styles for vignettes and other Bioconductor documents
biocViews
Categorized views of R package repositories
BiocWorkflowTools
Tools to aid the development of Bioconductor Workflow packages
bioDist
Different distance measures
biomaRt
Interface to BioMart databases (e.g. Ensembl, COSMIC, Wormbase and Gramene)
biomformat
An interface package for the BIOM file format
BioMVCClass
Model-View-Controller (MVC) Classes That Use Biobase
biomvRCNS
Copy Number study and Segmentation for multivariate biological data
BioNet
Routines for the functional analysis of biological networks
BioQC
Detect tissue heterogeneity in expression profiles with gene sets
BioSeqClass
Classification for Biological Sequences
biosigner
Signature discovery from omics data
Biostrings
String objects representing biological sequences, and matching algorithms
biosvd
Package for high-throughput data processing, outlier detection, noise removal and dynamic modeling
biovizBase
Basic graphic utilities for visualization of genomic data.
BiRewire
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
Bayesian Inference of Regulation of Transcriptional Activity
birte
Bayesian Inference of Regulatory Influence on Expression (biRte)
BiSeq
Processing and analyzing bisulfite sequencing data
BitSeq
Transcript expression inference and differential expression analysis for RNA-seq data
blima
Package for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level.
BPRMeth
Model higher-order methylation profiles
BRAIN
Baffling Recursive Algorithm for Isotope distributioN calculations
BrainStars
query gene expression data and plots from BrainStars (B*)
bridge
Bayesian Robust Inference for Differential Gene Expression
BridgeDbR
Code for using BridgeDb identifier mapping framework from within R
BrowserViz
BrowserViz: interactive R/browser graphics using websockets and JSON
BrowserVizDemo
BrowserVizDemo: How to subclass BrowserViz
BSgenome
Infrastructure for Biostrings-based genome data packages and support for efficient SNP representation
bsseq
Analyze, manage and store bisulfite sequencing data
BubbleTree
BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing data
BufferedMatrix
A matrix data storage object held in temporary files
BufferedMatrixMethods
Microarray Data related methods that utlize BufferedMatrix objects
bumphunter
Bump Hunter
BUS
Gene network reconstruction
CAFE
Chromosmal Aberrations Finder in Expression data
CAGEr
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
CALIB
Calibration model for estimating absolute expression levels from microarray data
CAMERA
Collection of annotation related methods for mass spectrometry data
canceR
A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC.
cancerclass
Development and validation of diagnostic tests from high-dimensional molecular data
CancerInSilico
An R interface for computational modeling of tumor progression
CancerMutationAnalysis
Cancer mutation analysis
CancerSubtypes
Cancer subtypes identification, validation and visualization based on genomic data
CAnD
Perform Chromosomal Ancestry Differences (CAnD) Analyses
caOmicsV
Visualization of multi-dimentional cancer genomics data
Cardinal
A mass spectrometry imaging toolbox for statistical analysis
casper
Characterization of Alternative Splicing based on Paired-End Reads
Category
Category Analysis
categoryCompare
Meta-analysis of high-throughput experiments using feature annotations
CausalR
Causal Reasoning Methods
ccmap
Combination Connectivity Mapping
CCPROMISE
PROMISE analysis with Canonical Correlation for Two Forms of High Dimensional Genetic Data
ccrepe
ccrepe_and_nc.score
cellGrowth
Fitting cell population growth models
cellHTS
Analysis of cell-based screens
cellHTS2
Analysis of cell-based screens - revised version of cellHTS
cellity
Quality Control for Single-Cell RNA-seq Data
CellMapper
Predict genes expressed selectively in specific cell types
CellNOptR
Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data.
cellTree
Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure
CexoR
An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates
CFAssay
Statistical analysis for the Colony Formation Assay
CGEN
An R package for analysis of case-control studies in genetic epidemiology
CGHbase
CGHbase: Base functions and classes for arrayCGH data analysis.
CGHcall
Calling aberrations for array CGH tumor profiles.
cghMCR
Find chromosome regions showing common gains/losses
CGHnormaliter
Normalization of array CGH data with imbalanced aberrations.
CGHregions
Dimension Reduction for Array CGH Data with Minimal Information Loss.
ChAMP
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
charm
Analysis of DNA methylation data from CHARM microarrays
ChemmineOB
R interface to a subset of OpenBabel functionalities
ChemmineR
Cheminformatics Toolkit for R
Chicago
CHiCAGO: Capture Hi-C Analysis of Genomic Organization
chimera
A package for secondary analysis of fusion products
ChIPComp
Quantitative comparison of multiple ChIP-seq datasets
chipenrich
Gene Set Enrichment For ChIP-seq Peak Data
ChIPpeakAnno
Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges
ChIPQC
Quality metrics for ChIPseq data
ChIPseeker
ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
chipseq
chipseq: A package for analyzing chipseq data
ChIPseqR
Identifying Protein Binding Sites in High-Throughput Sequencing Data
ChIPsim
Simulation of ChIP-seq experiments
ChIPXpress
ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles
chopsticks
The snp.matrix and X.snp.matrix classes
chroGPS
chroGPS: visualizing the epigenome
chromDraw
chromDraw is a R package for drawing the schemes of karyotypes in the linear and circular fashion.
ChromHeatMap
Heat map plotting by genome coordinate
chromPlot
Global visualization tool of genomic data
chromstaR
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data
CHRONOS
CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis
CINdex
Chromosome Instability Index
cisPath
Visualization and management of the protein-protein interaction networks.
ClassifyR
A framework for two-class classification problems, with applications to differential variability and differential distribution testing
cleanUpdTSeq
This package classifies putative polyadenylation sites as true or false/internally oligodT primed
cleaver
Cleavage of Polypeptide Sequences
clippda
A package for the clinical proteomic profiling data analysis
clipper
Gene Set Analysis Exploiting Pathway Topology
Clomial
Infers clonal composition of a tumor
Clonality
Clonality testing
clonotypeR
High throughput analysis of T cell antigen receptor sequences
clst
Classification by local similarity threshold
clstutils
Tools for performing taxonomic assignment.
clustComp
Clustering Comparison Package
clusterExperiment
Compare clusterings for single-cell sequencing
clusterProfiler
statistical analysis and visualization of functional profiles for genes and gene clusters
ClusterSignificance
The ClusterSignificance package provides tools to assess if clusters have a separation different from random or permuted data
clusterStab
Compute cluster stability scores for microarray data
CMA
Synthesis of microarray-based classification
CNAnorm
A normalization method for Copy Number Aberration in cancer samples
CNEr
CNE Detection and Visualization
cn.farms
cn.FARMS - factor analysis for copy number estimation
cn.mops
cn.mops - Mixture of Poissons for CNV detection in NGS data
CNORdt
Add-on to CellNOptR: Discretized time treatments
CNORfeeder
Integration of CellNOptR to add missing links
CNORfuzzy
Addon to CellNOptR: Fuzzy Logic
CNORode
ODE add-on to CellNOptR
CNPBayes
Bayesian mixture models for copy number polymorphisms
CNTools
Convert segment data into a region by sample matrix to allow for other high level computational analyses.
cnvGSA
Gene Set Analysis of (Rare) Copy Number Variants
CNVPanelizer
Reliable CNV detection in targeted sequencing applications
CNVrd2
CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.
CNVtools
A package to test genetic association with CNV data
cobindR
Finding Co-occuring motifs of transcription factor binding sites
CoCiteStats
Different test statistics based on co-citation.
codelink
Manipulation of Codelink microarray data
CODEX
A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing
CoGAPS
Coordinated Gene Activity in Pattern Sets
cogena
co-expressed gene-set enrichment analysis
coGPS
cancer outlier Gene Profile Sets
COHCAP
CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data
coMET
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns
COMPASS
Combinatorial Polyfunctionality Analysis of Single Cells
compcodeR
RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods
compEpiTools
Tools for computational epigenomics
CompGO
An R pipeline for .bed file annotation, comparing GO term enrichment between gene sets and data visualisation
ComplexHeatmap
Making Complex Heatmaps
CONFESS
Cell OrderiNg by FluorEScence Signal
ConsensusClusterPlus
ConsensusClusterPlus
consensusSeekeR
Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges
contiBAIT
Improves Early Build Genome Assemblies using Strand-Seq Data
conumee
Enhanced copy-number variation analysis using Illumina DNA methylation arrays
convert
Convert Microarray Data Objects
copa
Functions to perform cancer outlier profile analysis.
COPDSexualDimorphism
Sexual dimorphic and COPD differential analysis for gene expression and methylation.
copynumber
Segmentation of single- and multi-track copy number data by penalized least squares regression.
CopyNumber450k
R package for calling CNV from Illumina 450k methylation microarrays
CopywriteR
Copy number information from targeted sequencing using off-target reads
CoRegNet
CoRegNet : reconstruction and integrated analysis of co-regulatory networks
Cormotif
Correlation Motif Fit
CorMut
Detect the correlated mutations based on selection pressure
coRNAi
Analysis of co-knock-down RNAi data
CORREP
Multivariate Correlation Estimator and Statistical Inference Procedures.
cosmiq
cosmiq - COmbining Single Masses Into Quantities
COSNet
Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings
CountClust
Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models
covEB
Empirical Bayes estimate of block diagonal covariance matrices
CoverageView
Coverage visualization package for R
covRNA
Multivariate Analysis of Transcriptomic Data
cpvSNP
Gene set analysis methods for SNP association p-values that lie in genes in given gene sets
cqn
Conditional quantile normalization
CRImage
CRImage a package to classify cells and calculate tumour cellularity
CRISPRseek
Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems
crisprseekplus
crisprseekplus
CrispRVariants
Tools for counting and visualising mutations in a target location
crlmm
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays
crossmeta
Cross Platform Meta-Analysis of Microarray Data
CSAR
Statistical tools for the analysis of ChIP-seq data
csaw
ChIP-Seq Analysis with Windows
CSSP
ChIP-Seq Statistical Power
ctc
Cluster and Tree Conversion.
ctsGE
Clustering of Time Series Gene Expression data
cummeRbund
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
customProDB
Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search.
CVE
Cancer Variant Explorer
cycle
Significance of periodic expression pattern in time-series data
cytofkit
cytofkit: an integrated mass cytometry data analysis pipeline
CytoML
GatingML interface for openCyto
dada2
Accurate, high-resolution sample inference from amplicon sequencing data
dagLogo
dagLogo
daMA
Efficient design and analysis of factorial two-colour microarray data
DAPAR
Tools for the Differential Analysis of Proteins Abundance with R
DART
Denoising Algorithm based on Relevance network Topology
DASiR
Distributed Annotation System in R
DAVIDQuery
Retrieval from the DAVID bioinformatics data resource into R
DBChIP
Differential Binding of Transcription Factor with ChIP-seq
dcGSA
Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles
DChIPRep
DChIPRep - Analysis of chromatin modification ChIP-Seq data with replication
ddCt
The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)
ddgraph
Distinguish direct and indirect interactions with Graphical Modelling
debrowser
debrowser: Interactive Differential Expresion Analysis Browser
DECIPHER
Tools for curating, analyzing, and manipulating biological sequences
DeconRNASeq
Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq data
DEDS
Differential Expression via Distance Summary for Microarray Data
DeepBlueR
DeepBlueR
deepSNV
Detection of subclonal SNVs in deep sequencing data.
DEFormats
Differential gene expression data formats converter
DEGraph
Two-sample tests on a graph
DEGreport
Report of DEG analysis
DEGseq
Identify Differentially Expressed Genes from RNA-seq data
deltaGseg
deltaGseg
DeMAND
DeMAND
derfinder
Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
derfinderHelper
derfinder helper package
derfinderPlot
Plotting functions for derfinder
DESeq
Differential gene expression analysis based on the negative binomial distribution
DESeq2
Differential gene expression analysis based on the negative binomial distribution
destiny
Creates diffusion maps
DEsubs
DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments
DEXSeq
Inference of differential exon usage in RNA-Seq
dexus
DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates
DFP
Gene Selection
DiffBind
Differential Binding Analysis of ChIP-Seq peak data
diffGeneAnalysis
Performs differential gene expression Analysis
diffHic
Differential Analyis of Hi-C Data
DiffLogo
DiffLogo: A comparative visualisation of sequence motifs
diffloop
Differential DNA loop calling from ChIA-PET data
diggit
Inference of Genetic Variants Driving Cellular Phenotypes
Director
A dynamic visualization tool of multi-level data
DirichletMultinomial
Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
dks
The double Kolmogorov-Smirnov package for evaluating multiple testing procedures.
DMRcaller
Differentially Methylated Regions caller
DMRcate
Methylation array and sequencing spatial analysis methods
DMRforPairs
DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles
DNABarcodes
A tool for creating and analysing DNA barcodes used in Next Generation Sequencing multiplexing experiments
DNAcopy
DNA copy number data analysis
DNaseR
DNase I footprinting analysis of DNase-seq data
DNAshapeR
High-throughput prediction of DNA shape features
domainsignatures
Geneset enrichment based on InterPro domain signatures
doppelgangR
Identify likely duplicate samples from genomic or meta-data
DOQTL
Genotyping and QTL Mapping in DO Mice
DOSE
Disease Ontology Semantic and Enrichment analysis
DRIMSeq
Differential splicing and sQTL analyses with Dirichlet-multinomial model in RNA-Seq
DriverNet
Drivernet: uncovering somatic driver mutations modulating transcriptional networks in cancer
DrugVsDisease
Comparison of disease and drug profiles using Gene set Enrichment Analysis
dSimer
Integration of Disease Similarity Methods
DSS
Dispersion shrinakge for sequencing data.
DTA
Dynamic Transcriptome Analysis
dualKS
Dual KS Discriminant Analysis and Classification
DupChecker
a package for checking high-throughput genomic data redundancy in meta-analysis
dupRadar
Assessment of duplication rates in RNA-Seq datasets
dyebias
The GASSCO method for correcting for slide-dependent gene-specific dye bias
DynDoc
Dynamic document tools
EasyqpcR
EasyqpcR for low-throughput real-time quantitative PCR data analysis
easyRNASeq
Count summarization and normalization for RNA-Seq data
EBarrays
Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification
EBcoexpress
EBcoexpress for Differential Co-Expression Analysis
EBImage
Image processing and analysis toolbox for R
EBSEA
Exon Based Strategy for Expression Analysis of genes
EBSeq
An R package for gene and isoform differential expression analysis of RNA-seq data
EBSeqHMM
Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments
ecolitk
Meta-data and tools for E. coli
EDASeq
Exploratory Data Analysis and Normalization for RNA-Seq
EDDA
Experimental Design in Differential Abundance analysis
edge
Extraction of Differential Gene Expression
edgeR
Empirical Analysis of Digital Gene Expression Data in R
eegc
Engineering Evaluation by Gene Categorization (eegc)
EGAD
Extending guilt by association by degree
EGSEA
Ensemble of Gene Set Enrichment Analyses
eiR
Accelerated similarity searching of small molecules
eisa
Expression data analysis via the Iterative Signature Algorithm
ELBOW
ELBOW - Evaluating foLd change By the lOgit Way
ELMER
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
EMDomics
Earth Mover's Distance for Differential Analysis of Genomics Data
EmpiricalBrownsMethod
Uses Brown's method to combine p-values from dependent tests
ENCODExplorer
A compilation of ENCODE metadata
ENmix
Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip
EnrichedHeatmap
Making Enriched Heatmaps
EnrichmentBrowser
Seamless navigation through combined results of set-based and network-based enrichment analysis
ensembldb
Utilities to create and use an Ensembl based annotation database
ensemblVEP
R Interface to Ensembl Variant Effect Predictor
ENVISIONQuery
Retrieval from the ENVISION bioinformatics data portal into R
epigenomix
Epigenetic and gene transcription data normalization and integration with mixture models
epivizr
R Interface to epiviz web app
epivizrData
Data Management API for epiviz interactive visualization app
epivizrServer
WebSocket server infrastructure for epivizr apps and packages
epivizrStandalone
Run Epiviz Interactive Genomic Data Visualization App within R
erccdashboard
Assess Differential Gene Expression Experiments with ERCC Controls
erma
epigenomic road map adventures
esetVis
Visualizations of expressionSet Bioconductor object
eudysbiome
Cartesian plot and contingency test on 16S Microbial data
EWCE
Expression Weighted Celltype Enrichment
ExiMiR
R functions for the normalization of Exiqon miRNA array data
exomeCopy
Copy number variant detection from exome sequencing read depth
exomePeak
exome-based anlaysis of MeRIP-Seq data: peak calling and differential analysis
ExperimentHub
Client to access ExperimentHub resources
ExperimentHubData
Add resources to ExperimentHub
explorase
GUI for exploratory data analysis of systems biology data
ExpressionAtlas
Download datasets from EMBL-EBI Expression Atlas
ExpressionView
Visualize biclusters identified in gene expression data
fabia
FABIA: Factor Analysis for Bicluster Acquisition
facopy
Feature-based association and gene-set enrichment for copy number alteration analysis in cancer
factDesign
Factorial designed microarray experiment analysis
FamAgg
Pedigree Analysis and Familial Aggregation
farms
FARMS - Factor Analysis for Robust Microarray Summarization
fastLiquidAssociation
functions for genome-wide application of Liquid Association
fastseg
fastseg - a fast segmentation algorithm
fCCAC
functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets
fCI
f-divergence Cutoff Index for Differential Expression Analysis in Transcriptomics and Proteomics
fdrame
FDR adjustments of Microarray Experiments (FDR-AME)
FEM
Identification of Functional Epigenetic Modules
ffpe
Quality assessment and control for FFPE microarray expression data
FGNet
Functional Gene Networks derived from biological enrichment analyses
fgsea
Fast Gene Set Enrichment Analysis
FindMyFriends
Microbial Comparative Genomics in R
FISHalyseR
FISHalyseR a package for automated FISH quantification
FitHiC
Confidence estimation for intra-chromosomal contact maps
flagme
Analysis of Metabolomics GC/MS Data
flipflop
Fast lasso-based isoform prediction as a flow problem
flowAI
Automatic and interactive quality control for flow cytometry data
flowBeads
flowBeads: Analysis of flow bead data
flowBin
Combining multitube flow cytometry data by binning
flowcatchR
Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells
flowCHIC
Analyze flow cytometric data using histogram information
flowCL
Semantic labelling of flow cytometric cell populations
flowClean
flowClean
flowClust
Clustering for Flow Cytometry
flowCore
flowCore: Basic structures for flow cytometry data
flowCyBar
Analyze flow cytometric data using gate information
flowDensity
Sequential Flow Cytometry Data Gating
flowFit
Estimate proliferation in cell-tracking dye studies
flowFlowJo
Tools for extracting information from a FlowJo workspace and working with the data in the flowCore paradigm.
flowFP
Fingerprinting for Flow Cytometry
flowMap
Mapping cell populations in flow cytometry data for cross-sample comparisons using the Friedman-Rafsky Test
flowMatch
Matching and meta-clustering in flow cytometry
flowMeans
Non-parametric Flow Cytometry Data Gating
flowMerge
Cluster Merging for Flow Cytometry Data
flowPeaks
An R package for flow data clustering
flowPhyto
Methods for Continuous Flow Cytometry
flowPloidy
Analyze flow cytometer data to determine sample ploidy
flowPlots
flowPlots: analysis plots and data class for gated flow cytometry data
flowQ
Quality control for flow cytometry
flowQB
Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q, B and CV instrinsic calculations
FlowRepositoryR
FlowRepository R Interface
FlowSOM
Using self-organizing maps for visualization and interpretation of cytometry data
flowStats
Statistical methods for the analysis of flow cytometry data
flowTrans
Parameter Optimization for Flow Cytometry Data Transformation
flowType
Phenotyping Flow Cytometry Assays
flowUtils
Utilities for flow cytometry
flowViz
Visualization for flow cytometry
flowVS
Variance stabilization in flow cytometry (and microarrays)
flowWorkspace
Infrastructure for representing and interacting with the gated cytometry
fmcsR
Mismatch Tolerant Maximum Common Substructure Searching
focalCall
Detection of focal aberrations in DNA copy number data
FourCSeq
Package analyse 4C sequencing data
FRGEpistasis
Epistasis Analysis for Quantitative Traits by Functional Regression Model
frma
Frozen RMA and Barcode
frmaTools
Frozen RMA Tools
FunChIP
Clustering and Alignment of ChIP-Seq peaks based on their shapes
FunciSNP
Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs
gaga
GaGa hierarchical model for high-throughput data analysis
gage
Generally Applicable Gene-set Enrichment for Pathway Analysis
gaggle
Broadcast data between R and Gaggle
gaia
GAIA: An R package for genomic analysis of significant chromosomal aberrations.
GAprediction
Prediction of gestational age with Illumina HumanMethylation450 data
garfield
GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction
gaucho
Genetic Algorithms for Understanding Clonal Heterogeneity and Ordering
gcatest
Genotype Conditional Association TEST
gCMAP
Tools for Connectivity Map-like analyses
gCMAPWeb
A web interface for gene-set enrichment analyses
gCrisprTools
Suite of Functions for Pooled Crispr Screen QC and Analysis
gcrma
Background Adjustment Using Sequence Information
gdsfmt
R Interface to CoreArray Genomic Data Structure (GDS) Files
geecc
Gene Set Enrichment Analysis Extended to Contingency Cubes
GEM
GEM: fast association study for the interplay of Gene, Environment and Methylation
genArise
Microarray Analysis tool
genbankr
Parsing GenBank files into semantically useful objects
GeneAnswers
Integrated Interpretation of Genes
geneAttribution
Identification of candidate genes associated with genetic variation
GeneBreak
Gene Break Detection
GENE.E
Interact with GENE-E from R
GeneExpressionSignature
Gene Expression Signature based Similarity Metric
genefilter
genefilter: methods for filtering genes from high-throughput experiments
genefu
Computation of Gene Expression-Based Signatures in Breast Cancer
GeneGA
Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm
GeneGeneInteR
Tools for Testing Gene-Gene Interaction at the Gene Level
GeneMeta
MetaAnalysis for High Throughput Experiments
GeneNetworkBuilder
Build Regulatory Network from ChIP-chip/ChIP-seq and Expression Data
GeneOverlap
Test and visualize gene overlaps
geneplast
Evolutionary and plasticity analysis based on orthologous groups distribution
geneplotter
Graphics related functions for Bioconductor
geneRecommender
A gene recommender algorithm to identify genes coexpressed with a query set of genes
GeneRegionScan
GeneRegionScan
geneRxCluster
gRx Differential Clustering
GeneSelectMMD
Gene selection based on the marginal distributions of gene profiles that characterized by a mixture of three-component multivariate distributions
GeneSelector
Stability and Aggregation of ranked gene lists
GENESIS
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
geNetClassifier
Classify diseases and build associated gene networks using gene expression profiles
GeneticsDesign
Functions for designing genetics studies
GeneticsPed
Pedigree and genetic relationship functions
geneXtendeR
Optimal Gene Extensions From Histone Modification ChIP-seq Data
genoCN
genotyping and copy number study tools
GenoGAM
A GAM based framework for analysis of ChIP-Seq data
genomation
Summary, annotation and visualization of genomic data
GenomeGraphs
Plotting genomic information from Ensembl
GenomeInfoDb
Utilities for manipulating chromosome and other 'seqname' identifiers
genomeIntervals
Operations on genomic intervals
genomes
Genome sequencing project metadata
GenomicAlignments
Representation and manipulation of short genomic alignments
GenomicFeatures
Tools for making and manipulating transcript centric annotations
GenomicFiles
Distributed computing by file or by range
GenomicInteractions
R package for handling genomic interaction data
GenomicRanges
Representation and manipulation of genomic intervals and variables defined along a genome
GenomicTuples
Representation and Manipulation of Genomic Tuples
Genominator
Analyze, manage and store genomic data
genoset
A RangedSummarizedExperiment with methods for copy number analysis
genotypeeval
QA/QC of a gVCF or VCF file
genphen
A tool for quantification of associations between genotypes and phenotypes with statistical learning techniques such as random forests and support vector machines as well as with Bayesian inference using hierarchical models
GenRank
Candidate gene prioritization based on convergent evidence
GenVisR
Genomic Visualizations in R
GEOmetadb
A compilation of metadata from NCBI GEO
GEOquery
Get data from NCBI Gene Expression Omnibus (GEO)
GEOsearch
GEOsearch
GEOsubmission
Prepares microarray data for submission to GEO
gespeR
Gene-Specific Phenotype EstimatoR
GEWIST
Gene Environment Wide Interaction Search Threshold
GGBase
GGBase infrastructure for genetics of gene expression package GGtools
ggbio
Visualization tools for genomic data.
ggcyto
Visualize Cytometry data with ggplot
GGtools
software and data for analyses in genetics of gene expression
ggtree
an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
girafe
Genome Intervals and Read Alignments for Functional Exploration
GLAD
Gain and Loss Analysis of DNA
Glimma
Interactive HTML graphics
GlobalAncova
Calculates a global test for differential gene expression between groups
globalSeq
Testing for association between RNA-Seq and high-dimensional data
globaltest
Testing Groups of Covariates/Features for Association with a Response Variable, with Applications to Gene Set Testing
gmapR
An R interface to the GMAP/GSNAP/GSTRUCT suite
GMRP
GWAS-based Mendelian Randomization and Path Analyses
GOexpress
Visualise microarray and RNAseq data using gene ontology annotations
GOFunction
GO-function: deriving biologcially relevant functions from statistically significant functions
GoogleGenomics
R Client for Google Genomics API
GOpro
Find the most characteristic gene ontology terms for groups of human genes
goProfiles
goProfiles: an R package for the statistical analysis of functional profiles
GOSemSim
GO-terms Semantic Similarity Measures
goseq
Gene Ontology analyser for RNA-seq and other length biased data
GOSim
Computation of functional similarities between GO terms and gene products; GO enrichment analysis
GOstats
Tools for manipulating GO and microarrays.
GOsummaries
Word cloud summaries of GO enrichment analysis
GOTHiC
Binomial test for Hi-C data analysis
goTools
Functions for Gene Ontology database
gpls
Classification using generalized partial least squares
gprege
Gaussian Process Ranking and Estimation of Gene Expression time-series
gQTLBase
gQTLBase: infrastructure for eQTL, mQTL and similar studies
gQTLstats
gQTLstats: computationally efficient analysis for eQTL and allied studies
graph
graph: A package to handle graph data structures
GraphAlignment
GraphAlignment
GraphAT
Graph Theoretic Association Tests
graphite
GRAPH Interaction from pathway Topological Environment
GraphPAC
Identification of Mutational Clusters in Proteins via a Graph Theoretical Approach.
GRENITS
Gene Regulatory Network Inference Using Time Series
GreyListChIP
Grey Lists -- Mask Artefact Regions Based on ChIP Inputs
GRmetrics
Calculate growth-rate inhibition (GR) metrics
groHMM
GRO-seq Analysis Pipeline
GSALightning
Fast Permutation-based Gene Set Analysis
GSAR
Gene Set Analysis in R
GSCA
GSCA: Gene Set Context Analysis
GSEABase
Gene set enrichment data structures and methods
GSEAlm
Linear Model Toolset for Gene Set Enrichment Analysis
GSReg
Gene Set Regulation (GS-Reg)
GSRI
Gene Set Regulation Index
GSVA
Gene Set Variation Analysis for microarray and RNA-seq data
gtrellis
Genome Level Trellis Layout
GUIDEseq
GUIDE-seq analysis pipeline
Guitar
Guitar
Gviz
Plotting data and annotation information along genomic coordinates
gwascat
representing and modeling data in the EMBL-EBI GWAS catalog
GWASTools
Tools for Genome Wide Association Studies
h5vc
Managing alignment tallies using a hdf5 backend
hapFabia
hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data
Harman
The removal of batch effects from datasets using a PCA and constrained optimisation based technique
Harshlight
A "corrective make-up" program for microarray chips
HCsnip
Semi-supervised adaptive-height snipping of the Hierarchical Clustering tree
HDF5Array
An array-like container for convenient access and manipulation of HDF5 datasets
HDTD
Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD)
Heatplus
Heatmaps with row and/or column covariates and colored clusters
HelloRanges
Introduce *Ranges to bedtools users
HELP
Tools for HELP data analysis
HEM
Heterogeneous error model for identification of differentially expressed genes under multiple conditions
hiAnnotator
Functions for annotating GRanges objects
HIBAG
HLA Genotype Imputation with Attribute Bagging
hierGWAS
Asessing statistical significance in predictive GWA studies
HilbertCurve
Making 2D Hilbert Curve
HilbertVis
Hilbert curve visualization
HilbertVisGUI
HilbertVisGUI
hiReadsProcessor
Functions to process LM-PCR reads from 454/Illumina data
HiTC
High Throughput Chromosome Conformation Capture analysis
HMMcopy
Copy number prediction with correction for GC and mappability bias for HTS data
hopach
Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
hpar
Human Protein Atlas in R
HTqPCR
Automated analysis of high-throughput qPCR data
HTSanalyzeR
Gene set over-representation, enrichment and network analyses for high-throughput screens
HTSeqGenie
A NGS analysis pipeline.
htSeqTools
Quality Control, Visualization and Processing for High-Throughput Sequencing data
HTSFilter
Filter replicated high-throughput transcriptome sequencing data
HybridMTest
Hybrid Multiple Testing
hyperdraw
Visualizing Hypergaphs
hypergraph
A package providing hypergraph data structures
iASeq
iASeq: integrating multiple sequencing datasets for detecting allele-specific events
iBBiG
Iterative Binary Biclustering of Genesets
ibh
Interaction Based Homogeneity for Evaluating Gene Lists
iBMQ
integrated Bayesian Modeling of eQTL data
iCARE
A Tool for Individualized Coherent Absolute Risk Estimation (iCARE)
Icens
NPMLE for Censored and Truncated Data
iCheck
QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data
iChip
Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models
iClusterPlus
Integrative clustering of multi-type genomic data
iCOBRA
Comparison and Visualization of Ranking and Assignment Methods
IdeoViz
Plots data (continuous/discrete) along chromosomal ideogram
idiogram
idiogram
IdMappingAnalysis
ID Mapping Analysis
IdMappingRetrieval
ID Mapping Data Retrieval
iGC
An integrated analysis package of Gene expression and Copy number alteration
IHW
Independent Hypothesis Weighting
illuminaio
Parsing Illumina Microarray Output Files
imageHTS
Analysis of high-throughput microscopy-based screens
Imetagene
A graphical interface for the metagene package
ImmuneSpaceR
A Thin Wrapper around the ImmuneSpace Database
immunoClust
immunoClust - Automated Pipeline for Population Detection in Flow Cytometry
IMPCdata
Retrieves data from IMPC database
ImpulseDE
Detection of DE genes in time series data using impulse models
impute
impute: Imputation for microarray data
InPAS
Identification of Novel alternative PolyAdenylation Sites (PAS)
INPower
An R package for computing the number of susceptibility SNPs
inSilicoDb
Access to the InSilico Database
inSilicoMerging
Collection of Merging Techniques for Gene Expression Data
INSPEcT
Analysis of 4sU-seq and RNA-seq time-course data
intansv
Integrative analysis of structural variations
InteractionSet
Base Classes for Storing Genomic Interaction Data
interactiveDisplay
Package for enabling powerful shiny web displays of Bioconductor objects
interactiveDisplayBase
Base package for enabling powerful shiny web displays of Bioconductor objects
inveRsion
Inversions in genotype data
IONiseR
Quality Assessment Tools for Oxford Nanopore MinION data
iontree
Data management and analysis of ion trees from ion-trap mass spectrometry
iPAC
Identification of Protein Amino acid Clustering
IPO
Automated Optimization of XCMS Data Processing parameters
IPPD
Isotopic peak pattern deconvolution for Protein Mass Spectrometry by template matching
IRanges
Infrastructure for manipulating intervals on sequences
iSeq
Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising Models
isobar
Analysis and quantitation of isobarically tagged MSMS proteomics data
IsoGeneGUI
A graphical user interface to conduct a dose-response analysis of microarray data
ISoLDE
Integrative Statistics of alleLe Dependent Expression
isomiRs
Analyze isomiRs and miRNAs from small RNA-seq
ITALICS
ITALICS
iterativeBMA
The Iterative Bayesian Model Averaging (BMA) algorithm
iterativeBMAsurv
The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis
IVAS
Identification of genetic Variants affecting Alternative Splicing
jmosaics
Joint analysis of multiple ChIP-Seq data sets
joda
JODA algorithm for quantifying gene deregulation using knowledge
JunctionSeq
JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data
KCsmart
Multi sample aCGH analysis package using kernel convolution
kebabs
Kernel-Based Analysis Of Biological Sequences
KEGGgraph
KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
KEGGlincs
Visualize all edges within a KEGG pathway and overlay LINCS data [option]
keggorthology
graph support for KO, KEGG Orthology
KEGGprofile
An annotation and visualization package for multi-types and multi-groups expression data in KEGG pathway
KEGGREST
Client-side REST access to KEGG
kimod
A k-tables approach to integrate multiple Omics-Data
lapmix
Laplace Mixture Model in Microarray Experiments
LBE
Estimation of the false discovery rate.
ldblock
data structures for linkage disequilibrium measures in populations
LEA
LEA: an R package for Landscape and Ecological Association Studies
LedPred
Learning from DNA to Predict Enhancers
les
Identifying Differential Effects in Tiling Microarray Data
lfa
Logistic Factor Analysis for Categorical Data
limma
Linear Models for Microarray Data
limmaGUI
GUI for limma package with two color microarrays
LINC
co-expression of lincRNAs and protein-coding genes
Linnorm
Linear model and normality based transformation method (Linnorm)
LiquidAssociation
LiquidAssociation
lmdme
Linear Model decomposition for Designed Multivariate Experiments
LMGene
LMGene Software for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays
LOBSTAHS
Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences
logicFS
Identification of SNP Interactions
logitT
logit-t Package
lol
Lots Of Lasso
LOLA
Location overlap analysis for enrichment of genomic ranges
LowMACA
LowMACA - Low frequency Mutation Analysis via Consensus Alignment
LPE
Methods for analyzing microarray data using Local Pooled Error (LPE) method
LPEadj
A correction of the local pooled error (LPE) method to replace the asymptotic variance adjustment with an unbiased adjustment based on sample size.
lpNet
Linear Programming Model for Network Inference
lpsymphony
Symphony integer linear programming solver in R
lumi
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
LVSmiRNA
LVS normalization for Agilent miRNA data
LymphoSeq
Analyze high-throughput sequencing of T and B cell receptors
M3D
Identifies differentially methylated regions across testing groups
M3Drop
Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
maanova
Tools for analyzing Micro Array experiments
macat
MicroArray Chromosome Analysis Tool
maCorrPlot
Visualize artificial correlation in microarray data
made4
Multivariate analysis of microarray data using ADE4
MADSEQ
Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data
maftools
Summarize, Analyze and Visualize MAF files
maigesPack
Functions to handle cDNA microarray data, including several methods of data analysis
MAIT
Statistical Analysis of Metabolomic Data
makecdfenv
CDF Environment Maker
MANOR
CGH Micro-Array NORmalization
manta
Microbial Assemblage Normalized Transcript Analysis
MantelCorr
Compute Mantel Cluster Correlations
mAPKL
A Hybrid Feature Selection method for gene expression data
maPredictDSC
Phenotype prediction using microarray data: approach of the best overall team in the IMPROVER Diagnostic Signature Challenge
marray
Exploratory analysis for two-color spotted microarray data
maSigPro
Significant Gene Expression Profile Differences in Time Course Gene Expression Data
maskBAD
Masking probes with binding affinity differences
MassArray
Analytical Tools for MassArray Data
massiR
massiR: MicroArray Sample Sex Identifier
MassSpecWavelet
Mass spectrum processing by wavelet-based algorithms
MAST
Model-based Analysis of Single Cell Transcriptomics
matchBox
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
Obtain total affinity and occupancies for binding site matrices on a given sequence
matter
A framework for rapid prototyping with binary data on disk
MBAmethyl
Model-based analysis of DNA methylation data
MBASED
Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection
MBCB
MBCB (Model-based Background Correction for Beadarray)
mBPCR
Bayesian Piecewise Constant Regression for DNA copy number estimation
MBttest
Multiple Beta t-Tests
mcaGUI
Microbial Community Analysis GUI
MCRestimate
Misclassification error estimation with cross-validation
mdgsa
Multi Dimensional Gene Set Analysis.
mdqc
Mahalanobis Distance Quality Control for microarrays
MEAL
Perform methylation analysis
MeasurementError.cor
Measurement Error model estimate for correlation coefficient
MEDIPS
DNA IP-seq data analysis
MEDME
Modelling Experimental Data from MeDIP Enrichment
MEIGOR
MEIGO - MEtaheuristics for bIoinformatics Global Optimization
MergeMaid
Merge Maid
Mergeomics
Integrative network analysis of omics data
MeSHDbi
DBI to construct MeSH-related package from sqlite file
meshes
MeSH Enrichment and Semantic analyses
meshr
Tools for conducting enrichment analysis of MeSH
MeSHSim
MeSH(Medical Subject Headings) Semantic Similarity Measures
messina
Single-gene classifiers and outlier-resistant detection of differential expression for two-group and survival problems.
metaArray
Integration of Microarray Data for Meta-analysis
Metab
Metab: An R Package for a High-Throughput Analysis of Metabolomics Data Generated by GC-MS.
metabomxtr
A package to run mixture models for truncated metabolomics data with normal or lognormal distributions
MetaboSignal
MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways
metaCCA
Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide Association Studies Using Canonical Correlation Analysis
metagene
A package to produce metagene plots
metagenomeFeatures
Exploration of marker-gene sequence taxonomic annotations
metagenomeSeq
Statistical analysis for sparse high-throughput sequencing
metahdep
Hierarchical Dependence in Meta-Analysis
metaMS
MS-based metabolomics annotation pipeline
metaSeq
Meta-analysis of RNA-Seq count data in multiple studies
metaseqR
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.
metaX
An R package for metabolomic data analysis
MetCirc
MetCirc - a workflow to analyse and visualise metabolomics data
MethPed
A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes
MethTargetedNGS
Perform Methylation Analysis on Next Generation Sequencing Data
methVisual
Methods for visualization and statistics on DNA methylation data
methyAnalysis
DNA methylation data analysis and visualization
MethylAid
Visual and interactive quality control of large Illumina DNA Methylation array data sets
methylKit
DNA methylation analysis from high-throughput bisulfite sequencing results
MethylMix
MethylMix: Identifying methylation driven cancer genes.
methylMnM
detect different methylation level (DMR)
methylPipe
Base resolution DNA methylation data analysis
MethylSeekR
Segmentation of Bis-seq data
methylumi
Handle Illumina methylation data
Mfuzz
Soft clustering of time series gene expression data
MGFM
Marker Gene Finder in Microarray gene expression data
MGFR
Marker Gene Finder in RNA-seq data
mgsa
Model-based gene set analysis
MiChip
MiChip Parsing and Summarizing Functions
microRNA
Data and functions for dealing with microRNAs
MIMOSA
Mixture Models for Single-Cell Assays
MineICA
Analysis of an ICA decomposition obtained on genomics data
minet
Mutual Information NETworks
minfi
Analyze Illumina Infinium DNA methylation arrays
MinimumDistance
A Package for De Novo CNV Detection in Case-Parent Trios
MiPP
Misclassification Penalized Posterior Classification
MiRaGE
MiRNA Ranking by Gene Expression
miRcomp
Tools to assess and compare miRNA expression estimatation methods
mirIntegrator
Integrating microRNA expression into signaling pathways for pathway analysis
miRLAB
Dry lab for exploring miRNA-mRNA relationships
miRNAmeConverter
Convert miRNA Names to Different miRBase Versions
miRNApath
miRNApath: Pathway Enrichment for miRNA Expression Data
miRNAtap
miRNAtap: microRNA Targets - Aggregated Predictions
Mirsynergy
Mirsynergy
missMethyl
Analysing Illumina HumanMethylation BeadChip Data
mitoODE
Implementation of the differential equation model described in "Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay"
MLInterfaces
Uniform interfaces to R machine learning procedures for data in Bioconductor containers
MLP
MLP
MLSeq
Machine learning interface for RNA-Seq data
MMDiff
Statistical Testing for ChIP-Seq data sets
MMDiff2
Statistical Testing for ChIP-Seq data sets
mmnet
A metagenomic pipeline for systems biology
MmPalateMiRNA
Murine Palate miRNA Expression Analysis
MODA
MODA: MOdule Differential Analysis for weighted gene co-expression network
mogsa
Multiple omics data integrative clustering and gene set analysis
monocle
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
MoonlightR
Identify oncogenes and tumor suppressor genes from omics data
MoPS
MoPS - Model-based Periodicity Screening
mosaics
MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)
motifbreakR
A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites
MotifDb
An Annotated Collection of Protein-DNA Binding Sequence Motifs
motifRG
A package for discriminative motif discovery, designed for high throughput sequencing dataset
motifStack
Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
MotIV
Motif Identification and Validation
MPFE
Estimation of the amplicon methylation pattern distribution from bisulphite sequencing data
mQTL.NMR
Metabolomic Quantitative Trait Locus Mapping for 1H NMR data
msa
Multiple Sequence Alignment
MSGFgui
A shiny GUI for MSGFplus
MSGFplus
An interface between R and MS-GF+
msmsEDA
Exploratory Data Analysis of LC-MS/MS data by spectral counts
msmsTests
LC-MS/MS Differential Expression Tests
MSnbase
Base Functions and Classes for MS-based Proteomics
MSnID
Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications
msPurity
Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics
MSstats
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments
Mulcom
Calculates Mulcom test
MultiAssayExperiment
Create Classes and Functions for Managing Multiple Assays on Sets of Samples
multiClust
multiClust: An R-package for Identifying Biologically Relevant Clusters in Cancer Transcriptome Profiles
MultiDataSet
Implementation of the BRGE's (Bioinformatic Research Group in Epidemiology from Center for Research in Environmental Epidemiology) MultiDataSet and MethylationSet
MultiMed
Testing multiple biological mediators simultaneously
multiscan
R package for combining multiple scans
multtest
Resampling-based multiple hypothesis testing
muscle
Multiple Sequence Alignment with MUSCLE
MutationalPatterns
Studying patterns in base substitution catalogues
MVCClass
Model-View-Controller (MVC) Classes
mvGST
Multivariate and directional gene set testing
mygene
Access MyGene.Info_ services
myvariant
Accesses MyVariant.info variant query and annotation services
mzID
An mzIdentML parser for R
mzR
parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)
NanoStringDiff
Differential Expression Analysis of NanoString nCounter Data
NanoStringQCPro
Quality metrics and data processing methods for NanoString mRNA gene expression data
NarrowPeaks
Shape-based Analysis of Variation in ChIP-seq using Functional PCA
ncdfFlow
ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.
NCIgraph
Pathways from the NCI Pathways Database
neaGUI
An R package to perform the network enrichment analysis (NEA).
nem
(Dynamic) Nested Effects Models and Deterministic Effects Propagation Networks to reconstruct phenotypic hierarchies
netbenchmark
Benchmarking of several gene network inference methods
netbiov
A package for visualizing complex biological network
nethet
A bioconductor package for high-dimensional exploration of biological network heterogeneity
NetPathMiner
NetPathMiner for Biological Network Construction, Path Mining and Visualization
netprioR
A model for network-based prioritisation of genes
netresponse
Functional Network Analysis
NetSAM
Network Seriation And Modularization
networkBMA
Regression-based network inference using Bayesian Model Averaging
NGScopy
NGScopy: Detection of Copy Number Variations in Next Generation Sequencing sequencing
nnNorm
Spatial and intensity based normalization of cDNA microarray data based on robust neural nets
NOISeq
Exploratory analysis and differential expression for RNA-seq data
nondetects
Non-detects in qPCR data
normalize450K
Preprocessing of Illumina Infinium 450K data
NormqPCR
Functions for normalisation of RT-qPCR data
normr
Normalization and difference calling in ChIP-seq data
npGSEA
Permutation approximation methods for gene set enrichment analysis (non-permutation GSEA)
NTW
Predict gene network using an Ordinary Differential Equation (ODE) based method
nucleoSim
Generate synthetic nucleosome maps
nucleR
Nucleosome positioning package for R
nudge
Normal Uniform Differential Gene Expression detection
NuPoP
An R package for nucleosome positioning prediction
occugene
Functions for Multinomial Occupancy Distribution
OCplus
Operating characteristics plus sample size and local fdr for microarray experiments
odseq
Outlier detection in multiple sequence alignments
OGSA
Outlier Gene Set Analysis
oligo
Preprocessing tools for oligonucleotide arrays
oligoClasses
Classes for high-throughput arrays supported by oligo and crlmm
OLIN
Optimized local intensity-dependent normalisation of two-color microarrays
OLINgui
Graphical user interface for OLIN
omicade4
Multiple co-inertia analysis of omics datasets
OmicCircos
High-quality circular visualization of omics data
OmicsMarkeR
Classification and Feature Selection for 'Omics' Datasets
OncoScore
A tool to identify potentially oncogenic genes
OncoSimulR
Forward Genetic Simulation of Cancer Progression with Epistasis
oneChannelGUI
A graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops
ontoCAT
Ontology traversal and search
openCyto
Hierarchical Gating Pipeline for flow cytometry data
OperaMate
An R package of Data Importing, Processing and Analysis for Opera High Content Screening System
oposSOM
Comprehensive analysis of transciptome data
oppar
Outlier profile and pathway analysis in R
OrderedList
Similarities of Ordered Gene Lists
OrganismDbi
Software to enable the smooth interfacing of different database packages
OSAT
OSAT: Optimal Sample Assignment Tool
Oscope
Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq
OTUbase
Provides structure and functions for the analysis of OTU data
OutlierD
Outlier detection using quantile regression on the M-A scatterplots of high-throughput data
PAA
PAA (Protein Array Analyzer)
PADOG
Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)
paircompviz
Multiple comparison test visualization
pandaR
PANDA Algorithm
PAnnBuilder
Protein annotation data package builder
panp
Presence-Absence Calls from Negative Strand Matching Probesets
PANR
Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations
PanVizGenerator
Generate PanViz visualisations from your pangenome
PAPi
Predict metabolic pathway activity based on metabolomics data
parglms
support for parallelized estimation of GLMs/GEEs
parody
Parametric And Resistant Outlier DYtection
Path2PPI
Prediction of pathway-related protein-protein interaction networks
pathifier
Quantify deregulation of pathways in cancer
PathNet
An R package for pathway analysis using topological information
PathoStat
PathoStat Statistical Microbiome Analysis Package
pathRender
Render molecular pathways
pathVar
Methods to Find Pathways with Significantly Different Variability
pathview
a tool set for pathway based data integration and visualization
paxtoolsr
PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons
Pbase
Manipulating and exploring protein and proteomics data
pbcmc
Permutation-Based Confidence for Molecular Classification
pcaExplorer
Interactive Visualization of RNA-seq Data Using a Principal Components Approach
pcaGoPromoter
pcaGoPromoter is used to analyze DNA micro array data
pcaMethods
A collection of PCA methods
PCAN
Phenotype Consensus ANalysis (PCAN)
pcot2
Principal Coordinates and Hotelling's T-Square method
PCpheno
Phenotypes and cellular organizational units
pdInfoBuilder
Platform Design Information Package Builder
pdmclass
Classification of Microarray Samples using Penalized Discriminant Methods
PECA
Probe-level Expression Change Averaging
pepStat
Statistical analysis of peptide microarrays
pepXMLTab
Parsing pepXML files and filter based on peptide FDR.
PGA
An package for identification of novel peptides by customized database derived from RNA-Seq
PGSEA
Parametric Gene Set Enrichment Analysis
PharmacoGx
Analysis of Large-Scale Pharmacogenomic Data
phenoDist
Phenotypic distance measures
phenoTest
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
Statistical analysis of phenotypic data
philr
Phylogenetic partitioning based ILR transform for metagenomics data
phyloseq
Handling and analysis of high-throughput microbiome census data
Pi
Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene, Pathway and Network Level
piano
Platform for integrative analysis of omics data
pickgene
Adaptive Gene Picking for Microarray Expression Data Analysis
PICS
Probabilistic inference of ChIP-seq
Pigengene
Infers biological signatures from gene expression data
PING
Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data
pint
Pairwise INTegration of functional genomics data
pkgDepTools
Package Dependency Tools
plateCore
Statistical tools and data structures for plate-based flow cytometry
plethy
R framework for exploration and analysis of respirometry data
plgem
Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM)
plier
Implements the Affymetrix PLIER algorithm
PLPE
Local Pooled Error Test for Differential Expression with Paired High-throughput Data
plrs
Piecewise Linear Regression Splines (PLRS) for the association between DNA copy number and gene expression
plw
Probe level Locally moderated Weighted t-tests.
pmm
Parallel Mixed Model
podkat
Position-Dependent Kernel Association Test
polyester
Simulate RNA-seq reads
Polyfit
Add-on to DESeq to improve p-values and q-values
ppiStats
Protein-Protein Interaction Statistical Package
pqsfinder
Identification of potential quadruplex forming sequences
prada
Data analysis for cell-based functional assays
prebs
Probe region expression estimation for RNA-seq data for improved microarray comparability
PREDA
Position RElated Data Anlysis
predictionet
Inference for predictive networks designed for (but not limited to) genomic data
preprocessCore
A collection of pre-processing functions
Prize
Prize: an R package for prioritization estimation based on analytic hierarchy process
proBAMr
Generating SAM file for PSMs in shotgun proteomics data
PROcess
Ciphergen SELDI-TOF Processing
procoil
Prediction of Oligomerization of Coiled Coil Proteins
ProCoNA
Protein co-expression network analysis (ProCoNA).
proFIA
Preprocessing of FIA-HRMS data
profileScoreDist
Profile score distributions
pRoloc
A unifying bioinformatics framework for spatial proteomics
pRolocGUI
Interactive visualisation of spatial proteomics data
PROMISE
PRojection Onto the Most Interesting Statistical Evidence
PROPER
PROspective Power Evaluation for RNAseq
Prostar
Provides a GUI for DAPAR
prot2D
Statistical Tools for volume data from 2D Gel Electrophoresis
proteinProfiles
Protein Profiling
ProteomicsAnnotationHubData
Transform public proteomics data resources into Bioconductor Data Structures
proteoQC
An R package for proteomics data quality control
ProtGenerics
S4 generic functions for Bioconductor proteomics infrastructure
PSEA
Population-Specific Expression Analysis.
psichomics
Analyse and Visualise Alternative Splicing Data
PSICQUIC
Proteomics Standard Initiative Common QUery InterfaCe
psygenet2r
psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disorders
puma
Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)
PureCN
Copy number calling and SNV classification using targeted short read sequencing
pvac
PCA-based gene filtering for Affymetrix arrays
pvca
Principal Variance Component Analysis (PVCA)
Pviz
Peptide Annotation and Data Visualization using Gviz
PWMEnrich
PWM enrichment analysis
pwOmics
Pathway-based data integration of omics data
qcmetrics
A Framework for Quality Control
QDNAseq
Quantitative DNA sequencing for chromosomal aberrations
qpcrNorm
Data-driven normalization strategies for high-throughput qPCR data.
qpgraph
Estimation of genetic and molecular regulatory networks from high-throughput genomics data
qrqc
Quick Read Quality Control
qsea
IP-seq data analysis and vizualization
QUALIFIER
Quality Control of Gated Flow Cytometry Experiments
quantro
A test for when to use quantile normalization
quantsmooth
Quantile smoothing and genomic visualization of array data
QuartPAC
Identification of mutational clusters in protein quaternary structures.
QuasR
Quantify and Annotate Short Reads in R
QuaternaryProd
Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs
QUBIC
An R package for qualitative biclustering in support of gene co-expression analyses
qusage
qusage: Quantitative Set Analysis for Gene Expression
qvalue
Q-value estimation for false discovery rate control
R3CPET
3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process
r3Cseq
Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)
R453Plus1Toolbox
A package for importing and analyzing data from Roche's Genome Sequencer System
R4RNA
An R package for RNA visualization and analysis
rain
Rhythmicity Analysis Incorporating Non-parametric Methods
rama
Robust Analysis of MicroArrays
RamiGO
AmiGO visualize R interface
randPack
Randomization routines for Clinical Trials
RankProd
Rank Product method for identifying differentially expressed genes with application in meta-analysis
RareVariantVis
Visualization of rare variants in whole genome sequencing data
Rariant
Identification and Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies
RbcBook1
Support for Springer monograph on Bioconductor
RBGL
An interface to the BOOST graph library
RBioinf
RBioinf
rBiopaxParser
Parses BioPax files and represents them in R
RBM
RBM: a R package for microarray and RNA-Seq data analysis
Rbowtie
R bowtie wrapper
rbsurv
Robust likelihood-based survival modeling with microarray data
Rcade
R-based analysis of ChIP-seq And Differential Expression - a tool for integrating a count-based ChIP-seq analysis with differential expression summary data
RCAS
RNA Centric Annotation System
RCASPAR
A package for survival time prediction based on a piecewise baseline hazard Cox regression model.
rcellminer
rcellminer: Molecular Profiles and Drug Response for the NCI-60 Cell Lines
rCGH
Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data
Rchemcpp
Similarity measures for chemical compounds
RchyOptimyx
Optimyzed Cellular Hierarchies for Flow Cytometry
Rcpi
Toolkit for Compound-Protein Interaction in Drug Discovery
RCy3
Display and manipulate graphs in Cytoscape >= 3.3.0
RCyjs
Display and manipulate graphs in cytoscape.js
RCytoscape
Display and manipulate graphs in Cytoscape
RDAVIDWebService
An R Package for retrieving data from DAVID into R objects using Web Services API.
rDGIdb
R Wrapper for DGIdb
Rdisop
Decomposition of Isotopic Patterns
RDRToolbox
A package for nonlinear dimension reduction with Isomap and LLE.
ReactomePA
Reactome Pathway Analysis
readat
Functionality to Read and Manipulate SomaLogic ADAT files
ReadqPCR
Read qPCR data
reb
Regional Expression Biases
recount
Explore and download data from the recount project
recoup
An R package for the creation of complex genomic profile plots
RedeR
Interactive visualization and manipulation of nested networks
REDseq
Analysis of high-throughput sequencing data processed by restriction enzyme digestion
RefNet
A queryable collection of molecular interactions, from many sources
RefPlus
A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods.
regioneR
Association analysis of genomic regions based on permutation tests
regionReport
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
regsplice
Lasso-Based Methods for Detection of Differential Exon Usage
Repitools
Epigenomic tools
ReportingTools
Tools for making reports in various formats
ReQON
Recalibrating Quality Of Nucleotides
Resourcerer
Reads annotation data from TIGR Resourcerer or convert the annotation data into Bioconductor data pacakge.
rfPred
Assign rfPred functional prediction scores to a missense variants list
rGADEM
de novo motif discovery
RGalaxy
Make an R function available in the Galaxy web platform
RGraph2js
Convert a Graph into a D3js Script
Rgraphviz
Provides plotting capabilities for R graph objects
rGREAT
Client for GREAT Analysis
RGSEA
Random Gene Set Enrichment Analysis
rgsepd
Gene Set Enrichment / Projection Displays
rhdf5
HDF5 interface to R
Rhtslib
HTSlib high-throughput sequencing library as an R package
rHVDM
Hidden Variable Dynamic Modeling
RiboProfiling
Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation
riboSeqR
Analysis of sequencing data from ribosome profiling experiments
RImmPort
RImmPort: Enabling Ready-for-analysis Immunology Research Data
Ringo
R Investigation of ChIP-chip Oligoarrays
RIPSeeker
RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments
Risa
Converting experimental metadata from ISA-tab into Bioconductor data structures
RLMM
A Genotype Calling Algorithm for Affymetrix SNP Arrays
Rmagpie
MicroArray Gene-expression-based Program In Error rate estimation
RMAPPER
R interface to the MAPPER database of transcription factor binding sites
RMassBank
Workflow to process tandem MS files and build MassBank records
rMAT
R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data.
RmiR
Package to work with miRNAs and miRNA targets with R
RNAinteract
Estimate Pairwise Interactions from multidimensional features
RNAither
Statistical analysis of high-throughput RNAi screens
RNAprobR
An R package for analysis of massive parallel sequencing based RNA structure probing data
rnaseqcomp
Benchmarks for RNA-seq Quantification Pipelines
rnaSeqMap
rnaSeq secondary analyses
RNASeqPower
Sample size for RNAseq studies
RnaSeqSampleSize
RnaSeqSampleSize
RnBeads
RnBeads
Rnits
R Normalization and Inference of Time Series data
roar
Identify differential APA usage from RNA-seq alignments
ROC
utilities for ROC, with uarray focus
Roleswitch
Infer miRNA-mRNA interactions using paired expression data from a single sample
Rolexa
Statistical analysis of Solexa sequencing data
rols
An R interface to the Ontology Lookup Service
ROntoTools
R Onto-Tools suite
ropls
PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data
ROTS
Reproducibility-Optimized Test Statistic
RPA
RPA: Robust Probabilistic Averaging for probe-level analysis
RpsiXML
R interface to PSI-MI 2.5 files
rpx
R Interface to the ProteomeXchange Repository
Rqc
Quality Control Tool for High-Throughput Sequencing Data
rqubic
Qualitative biclustering algorithm for expression data analysis in R
rRDP
Interface to the RDP Classifier
RRHO
Inference on agreement between ordered lists
Rsamtools
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
rsbml
R support for SBML, using libsbml
rSFFreader
rSFFreader reads in sff files generated by Roche 454 and Life Sciences Ion Torrent sequencers
Rsubread
Subread sequence alignment for R
RSVSim
RSVSim: an R/Bioconductor package for the simulation of structural variations
rTANDEM
Interfaces the tandem protein identification algorithm in R
RTCA
Open-source toolkit to analyse data from xCELLigence System (RTCA)
RTCGA
The Cancer Genome Atlas Data Integration
RTCGAToolbox
A new tool for exporting TCGA Firehose data
RTN
Reconstruction of transcriptional networks and analysis of master regulators
RTopper
This package is designed to perform Gene Set Analysis across multiple genomic platforms
rtracklayer
R interface to genome browsers and their annotation tracks
Rtreemix
Rtreemix: Mutagenetic trees mixture models.
rTRM
Identification of transcriptional regulatory modules from PPI networks
rTRMui
A shiny user interface for rTRM
RUVcorr
Removal of unwanted variation for gene-gene correlations and related analysis
RUVnormalize
RUV for normalization of expression array data
RUVSeq
Remove Unwanted Variation from RNA-Seq Data
RWebServices
Expose R functions as web services through Java/Axis/Apache
S4Vectors
S4 implementation of vectors and lists
safe
Significance Analysis of Function and Expression
sagenhaft
Collection of functions for reading and comparing SAGE libraries
SAGx
Statistical Analysis of the GeneChip
SamSPECTRAL
Identifies cell population in flow cytometry data.
sangerseqR
Tools for Sanger Sequencing Data in R
SANTA
Spatial Analysis of Network Associations
sapFinder
A package for variant peptides detection and visualization in shotgun proteomics.
saps
Significance Analysis of Prognostic Signatures
savR
Parse and analyze Illumina SAV files
sbgr
R Client for Seven Bridges Genomics API
SBMLR
SBML-R Interface and Analysis Tools
SC3
Single-Cell Consensus Clustering
SCAN.UPC
Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
scater
Single-cell analysis toolkit for gene expression data in R
scde
Single Cell Differential Expression
ScISI
In Silico Interactome
scran
Methods for Single-Cell RNA-Seq Data Analysis
scsR
SiRNA correction for seed mediated off-target effect
segmentSeq
Methods for identifying small RNA loci from high-throughput sequencing data
SELEX
Functions for analyzing SELEX-seq data
SemDist
Information Accretion-based Function Predictor Evaluation
SEPA
SEPA
seq2pathway
a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data
SeqArray
Big Data Management of Whole-genome Sequence Variant Calls
seqbias
Estimation of per-position bias in high-throughput sequencing data
seqCNA
Copy number analysis of high-throughput sequencing cancer data
SeqGSEA
Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
seqLogo
Sequence logos for DNA sequence alignments
seqPattern
Visualising oligonucleotide patterns and motif occurrences across a set of sorted sequences
seqplots
An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps
seqTools
Analysis of nucleotide, sequence and quality content on fastq files.
SeqVarTools
Tools for variant data
sevenbridges
R Client for Seven Bridges Platform API and CWL Tool Builder in R
SGSeq
Splice event prediction and quantification from RNA-seq data
shinyMethyl
Interactive visualization for Illumina methylation arrays
shinyTANDEM
Provides a GUI for rTANDEM
ShortRead
FASTQ input and manipulation
SICtools
Find SNV/Indel differences between two bam files with near relationship
sigaR
Statistics for Integrative Genomics Analyses in R
SigCheck
Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadata
SigFuge
SigFuge
siggenes
Multiple testing using SAM and Efron's empirical Bayes approaches
sights
Statistics and dIagnostic Graphs for HTS
signeR
signeR
sigPathway
Pathway Analysis
sigsquared
Gene signature generation for functionally validated signaling pathways
SIM
Integrated Analysis on two human genomic datasets
SIMAT
GC-SIM-MS data processing and alaysis tool
SimBindProfiles
Similar Binding Profiles
similaRpeak
Metrics to estimate a level of similarity between two ChIP-Seq profiles
SIMLR
SIMLR: Single-cell Interpretation via Multi-kernel LeaRning
simpleaffy
Very simple high level analysis of Affymetrix data
simulatorZ
Simulator for Collections of Independent Genomic Data Sets
sincell
R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data
SISPA
SISPA: Method for Sample Integrated Set Profile Analysis
sizepower
Sample Size and Power Calculation in Micorarray Studies
SJava
The Omegahat interface for R and Java
skewr
Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip
SLGI
Synthetic Lethal Genetic Interaction
SLqPCR
Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH
SMAP
A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling
SMITE
Significance-based Modules Integrating the Transcriptome and Epigenome
SNAGEE
Signal-to-Noise applied to Gene Expression Experiments
snapCGH
Segmentation, normalisation and processing of aCGH data.
snm
Supervised Normalization of Microarrays
SNPchip
Visualizations for copy number alterations
SNPediaR
Query data from SNPedia
SNPhood
SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data
SNPRelate
Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data
snpStats
SnpMatrix and XSnpMatrix classes and methods
soGGi
Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots Summarised Over Grouped Genomic Intervals
SomatiCA
SomatiCA: identifying, characterizing, and quantifying somatic copy number aberrations from cancer genome sequencing
SomaticSignatures
Somatic Signatures
SpacePAC
Identification of Mutational Clusters in 3D Protein Space via Simulation.
spade
SPADE -- An analysis and visualization tool for Flow Cytometry
specL
specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics
SpeCond
Condition specific detection from expression data
SPEM
S-system parameter estimation method
SPIA
Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
SpidermiR
SpidermiR: An R/Bioconductor package for integrative network analysis with miRNA data
spikeLI
Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool
spkTools
Methods for Spike-in Arrays
splicegear
splicegear
spliceR
Classification of alternative splicing and prediction of coding potential from RNA-seq data.
spliceSites
A bioconductor package for exploration of alignment gap positions from RNA-seq data
SplicingGraphs
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
splineTCDiffExpr
Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction
splineTimeR
Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction
SPLINTER
Splice Interpreter Of Transcripts
splots
Visualization of high-throughput assays in microtitre plate or slide format
spotSegmentation
Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots
SQUADD
Add-on of the SQUAD Software
SRAdb
A compilation of metadata from NCBI SRA and tools
sRAP
Simplified RNA-Seq Analysis Pipeline
SRGnet
SRGnet An R package for studying synergistic response genes from transcriptomics data
sscore
S-Score Algorithm for Affymetrix Oligonucleotide Microarrays
sscu
Strength of Selected Codon Usage
sSeq
Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size
ssize
Estimate Microarray Sample Size
SSPA
General Sample Size and Power Analysis for Microarray and Next-Generation Sequencing Data
ssviz
A small RNA-seq visualizer and analysis toolkit
STAN
The genomic STate ANnotation package
staRank
Stability Ranking
StarBioTrek
StarBioTrek
Starr
Simple tiling array analysis of Affymetrix ChIP-chip data
STATegRa
Classes and methods for multi-omics data integration
statTarget
Statistical Analysis of Metabolite Profile
stepNorm
Stepwise normalization functions for cDNA microarrays
stepwiseCM
Stepwise Classification of Cancer Samples using High-dimensional Data Sets
Streamer
Enabling stream processing of large files
STRINGdb
STRINGdb (Search Tool for the Retrieval of Interacting proteins database)
subSeq
Subsampling of high-throughput sequencing count data
SummarizedExperiment
SummarizedExperiment container
supraHex
supraHex: a supra-hexagonal map for analysing tabular omics data
survcomp
Performance Assessment and Comparison for Survival Analysis
Sushi
Tools for visualizing genomics data
sva
Surrogate Variable Analysis
SVAPLSseq
SVAPLSseq-An R package to adjust for the hidden factors of variability in differential gene expression studies based on RNAseq data
SVM2CRM
SVM2CRM: support vector machine for cis-regulatory elements detections
SWATH2stats
Transform and Filter SWATH Data for Statistical Packages
SwathXtend
SWATH extended library generation and satistical data analysis
SwimR
SwimR: A Suite of Analytical Tools for Quantification of C. elegans Swimming Behavior
switchBox
Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair (KTSP) algorithm
switchde
Switch-like differential expression across single-cell trajectories
synapter
Label-free data analysis pipeline for optimal identification and quantitation
synergyfinder
Calculate and Visualize Synergy Scores for Drug Combinations
synlet
Hits Selection for Synthetic Lethal RNAi Screen Data
systemPipeR
systemPipeR: NGS workflow and report generation environment
TargetScore
TargetScore: Infer microRNA targets using microRNA-overexpression data and sequence information
TargetSearch
A package for the analysis of GC-MS metabolite profiling data
TarSeqQC
TARgeted SEQuencing Experiment Quality Control
TCC
TCC: Differential expression analysis for tag count data with robust normalization strategies
TCGAbiolinks
TCGAbiolinks: An R/Bioconductor package for integrative analysis with TCGA data
TDARACNE
Network reverse engineering from time course data.
TEQC
Quality control for target capture experiments
ternarynet
Ternary Network Estimation
TFBSTools
Software Package for Transcription Factor Binding Site (TFBS) Analysis
tigre
Transcription factor Inference through Gaussian process Reconstruction of Expression
tilingArray
Transcript mapping with high-density oligonucleotide tiling arrays
timecourse
Statistical Analysis for Developmental Microarray Time Course Data
TIN
Transcriptome instability analysis
TitanCNA
Subclonal copy number and LOH prediction from whole genome sequencing of tumours
tkWidgets
R based tk widgets
tofsims
Import, process and analysis of Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) imaging data
ToPASeq
Package for Topology-based Pathway Analysis of RNASeq data
topGO
Enrichment Analysis for Gene Ontology
TPP
Analyze thermal proteome profiling (TPP) experiments
tracktables
Build IGV tracks and HTML reports
trackViewer
A bioconductor package with minimalist design for drawing elegant tracks or lollipop plot
transcriptR
An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification
tRanslatome
Comparison between multiple levels of gene expression
TransView
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
traseR
GWAS trait-associated SNP enrichment analyses in genomic intervals
triform
Triform finds enriched regions (peaks) in transcription factor ChIP-sequencing data
trigger
Transcriptional Regulatory Inference from Genetics of Gene ExpRession
trio
Testing of SNPs and SNP Interactions in Case-Parent Trio Studies
triplex
Search and visualize intramolecular triplex-forming sequences in DNA
TRONCO
TRONCO, an R package for TRanslational ONCOlogy
TSCAN
TSCAN: Tools for Single-Cell ANalysis
tspair
Top Scoring Pairs for Microarray Classification
TSSi
Transcription Start Site Identification
TurboNorm
A fast scatterplot smoother suitable for microarray normalization
TVTB
TVTB: The VCF Tool Box
tweeDEseq
RNA-seq data analysis using the Poisson-Tweedie family of distributions
twilight
Estimation of local false discovery rate
tximport
Import and summarize transcript-level estimates for gene-level analysis
TypeInfo
Optional Type Specification Prototype
UNDO
Unsupervised Deconvolution of Tumor-Stromal Mixed Expressions
unifiedWMWqPCR
Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data
UniProt.ws
R Interface to UniProt Web Services
Uniquorn
Identification of cancer cell lines based on their weighted mutational/ variational fingerprint
uSORT
uSORT: A self-refining ordering pipeline for gene selection
VanillaICE
A Hidden Markov Model for high throughput genotyping arrays
variancePartition
Quantify and interpret divers of variation in multilevel gene expression experiments
VariantAnnotation
Annotation of Genetic Variants
VariantFiltering
Filtering of coding and non-coding genetic variants
VariantTools
Tools for Working with Genetic Variants
vbmp
Variational Bayesian Multinomial Probit Regression
Vega
An R package for copy number data segmentation
VegaMC
VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer
viper
Virtual Inference of Protein-activity by Enriched Regulon analysis
virtualArray
Build virtual array from different microarray platforms
vsn
Variance stabilization and calibration for microarray data
vtpnet
variant-transcription factor-phenotype networks
wateRmelon
Illumina 450 methylation array normalization and metrics
wavClusteR
Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data
waveTiling
Wavelet-Based Models for Tiling Array Transcriptome Analysis
weaver
Tools and extensions for processing Sweave documents
webbioc
Bioconductor Web Interface
widgetTools
Creates an interactive tcltk widget
XBSeq
Test for differential expression for RNA-seq data
xcms
LC/MS and GC/MS Data Analysis
XDE
XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression
xmapbridge
Export plotting files to the xmapBridge for visualisation in X:Map
xps
Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays
XVector
Representation and manpulation of external sequences
yamss
Tools for high-throughput metabolomics
YAPSA
Yet Another Package for Signature Analysis
yaqcaffy
Affymetrix expression data quality control and reproducibility analysis
yarn
YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization
zlibbioc
An R packaged zlib-1.2.5