DESeq2: Differential gene expression analysis based on the negative binomial distribution
Version 1.16.1

Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.

AuthorMichael Love, Simon Anders, Wolfgang Huber
Bioconductor views ChIPSeq DifferentialExpression GeneExpression RNASeq SAGE Sequencing Transcription
Date of publicationNone
MaintainerMichael Love <michaelisaiahlove@gmail.com>
LicenseLGPL (>= 3)
Version1.16.1
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")

Getting started

Package overview
Analyzing RNA-seq data with DESeq2

Popular man pages

DESeqDataSet: DESeqDataSet object and constructors
estimateSizeFactors: Estimate the size factors for a 'DESeqDataSet'
fpkm: FPKM: fragments per kilobase per million mapped fragments
plotMA: MA-plot from base means and log fold changes
results: Extract results from a DESeq analysis
rlog: Apply a 'regularized log' transformation
varianceStabilizingTransformation: Apply a variance stabilizing transformation (VST) to the...
See all...

All man pages Function index File listing

Man pages

coef: Extract a matrix of model coefficients/standard errors
collapseReplicates: Collapse technical replicates in a RangedSummarizedExperiment...
counts: Accessors for the 'counts' slot of a DESeqDataSet object.
DESeq: Differential expression analysis based on the Negative...
DESeq2-package: DESeq2 package for differential analysis of count data
DESeqDataSet: DESeqDataSet object and constructors
DESeqResults: DESeqResults object and constructor
DESeqTransform: DESeqTransform object and constructor
design: Accessors for the 'design' slot of a DESeqDataSet object.
dispersionFunction: Accessors for the 'dispersionFunction' slot of a DESeqDataSet...
dispersions: Accessor functions for the dispersion estimates in a...
estimateBetaPriorVar: Steps for estimating the beta prior variance
estimateDispersions: Estimate the dispersions for a DESeqDataSet
estimateDispersionsGeneEst: Low-level functions to fit dispersion estimates
estimateSizeFactors: Estimate the size factors for a 'DESeqDataSet'
estimateSizeFactorsForMatrix: Low-level function to estimate size factors with robust...
fpkm: FPKM: fragments per kilobase per million mapped fragments
fpm: FPM: fragments per million mapped fragments
lfcShrink: Shrink log2 fold changes
makeExampleDESeqDataSet: Make a simulated DESeqDataSet
nbinomLRT: Likelihood ratio test (chi-squared test) for GLMs
nbinomWaldTest: Wald test for the GLM coefficients
normalizationFactors: Accessor functions for the normalization factors in a...
normalizeGeneLength: Normalize for gene length
normTransform: Normalized counts transformation
plotCounts: Plot of normalized counts for a single gene
plotDispEsts: Plot dispersion estimates
plotMA: MA-plot from base means and log fold changes
plotPCA: Sample PCA plot for transformed data
plotSparsity: Sparsity plot
replaceOutliers: Replace outliers with trimmed mean
results: Extract results from a DESeq analysis
rlog: Apply a 'regularized log' transformation
show: Show method for DESeqResults objects
sizeFactors: Accessor functions for the 'sizeFactors' information in a...
summary: Summarize DESeq results
unmix: Unmix samples using loss in a variance stabilized space
varianceStabilizingTransformation: Apply a variance stabilizing transformation (VST) to the...
vst: Quickly estimate dispersion trend and apply a variance...

Functions

DESeq Man page Source code
DESeq2-package Man page
DESeqDataSet Man page Source code
DESeqDataSet-class Man page Man page
DESeqDataSetFromHTSeqCount Man page Man page Source code
DESeqDataSetFromMatrix Man page Man page Source code
DESeqDataSetFromTximport Man page Source code
DESeqParallel Source code
DESeqResults Man page Source code
DESeqResults-class Man page Man page
DESeqTransform Man page Source code
DESeqTransform-class Man page Man page
addAllContrasts Source code
averagePriorsOverLevels Source code
buildDataFrameWithNARows Source code
buildMatrixWithNARows Source code
buildMatrixWithZeroRows Source code
calculateCooksDistance Source code
checkContrast Source code
checkForExperimentalReplicates Source code
checkFullRank Source code
checkLRT Source code
cleanContrast Source code
coef Man page
coef.DESeqDataSet Man page Source code
collapseReplicates Man page Source code
counts Man page Man page
counts,DESeqDataSet-method Man page
counts.DESeqDataSet Source code
counts<-,DESeqDataSet,matrix-method Man page
covarianceMatrix Source code
design Man page Man page
design,DESeqDataSet-method Man page
design.DESeqDataSet Source code
design<-,DESeqDataSet,formula-method Man page
designAndArgChecker Source code
dispersionFunction Man page Man page Man page
dispersionFunction,DESeqDataSet-method Man page
dispersionFunction.DESeqDataSet Source code
dispersionFunction<- Man page
dispersionFunction<-,DESeqDataSet,function-method Man page
dispersions Man page Man page Man page
dispersions,DESeqDataSet-method Man page
dispersions.DESeqDataSet Source code
dispersions<- Man page
dispersions<-,DESeqDataSet,numeric-method Man page
estimateBetaPriorVar Man page Source code
estimateDispersions Man page
estimateDispersions,DESeqDataSet-method Man page
estimateDispersions.DESeqDataSet Source code
estimateDispersionsFit Man page Man page Source code
estimateDispersionsGeneEst Man page Source code
estimateDispersionsMAP Man page Man page Source code
estimateDispersionsPriorVar Man page Man page Source code
estimateMLEForBetaPriorVar Man page Man page Source code
estimateNormFactors Source code
estimateSizeFactors Man page
estimateSizeFactors,DESeqDataSet-method Man page
estimateSizeFactors.DESeqDataSet Source code
estimateSizeFactorsForMatrix Man page Source code
estimateSizeFactorsIterate Source code
fitBeta Source code
fitBetaWrapper Source code
fitDisp Source code
fitDispGrid Source code
fitDispGridWrapper Source code
fitDispWrapper Source code
fitGLMsWithPrior Source code
fitNbinomGLMs Source code
fitNbinomGLMsOptim Source code
fpkm Man page Source code
fpm Man page Source code
getAndCheckWeights Source code
getBaseMeansAndVariances Source code
getCoef Source code
getCoefSE Source code
getContrast Source code
getDesignFactors Source code
getModelMatrix Source code
getPvalue Source code
getSizeOrNormFactors Source code
getStat Source code
getVarianceStabilizedData Man page Man page Source code
lastCoefName Source code
lfcShrink Man page Source code
linearModelMu Source code
linearModelMuNormalized Source code
localDispersionFit Source code
makeExampleDESeqDataSet Man page Source code
makeExpandedModelMatrix Source code
makeWaldTest Source code
matchUpperQuantileForVariance Source code
matchWeightedUpperQuantileForVariance Source code
matrixToList Source code
mleContrast Source code
modelMatrixGroups Source code
momentsDispEstimate Source code
nOrMoreInCell Source code
nbinomLRT Man page Source code
nbinomLogLike Source code
nbinomWaldTest Man page Source code
normTransform Man page Source code
normalizationFactors Man page Man page Man page
normalizationFactors,DESeqDataSet-method Man page
normalizationFactors.DESeqDataSet Source code
normalizationFactors<- Man page
normalizationFactors<-,DESeqDataSet,matrix-method Man page
normalizeGeneLength Man page Source code
parametricDispersionFit Source code
plotCounts Man page Source code
plotDispEsts Man page
plotDispEsts,DESeqDataSet-method Man page
plotDispEsts.DESeqDataSet Source code
plotMA Man page Man page
plotMA,DESeqDataSet-method Man page
plotMA,DESeqResults-method Man page
plotMA.DESeqDataSet Source code
plotMA.DESeqResults Source code
plotPCA Man page
plotPCA,DESeqTransform-method Man page
plotPCA.DESeqTransform Source code
plotSparsity Man page Source code
pvalueAdjustment Source code
recordMaxCooks Source code
refitWithoutOutliers Source code
removeResults Man page Man page Source code
renameModelMatrixColumns Source code
replaceOutliers Man page Source code
replaceOutliersWithTrimmedMean Man page Man page
results Man page Source code
resultsNames Man page Man page Source code
rlog Man page Source code
rlogData Source code
rlogTransformation Man page Man page
robustMethodOfMomentsDisp Source code
roughDispEstimate Source code
sanitizeColData Source code
sanitizeRowRanges Source code
show Man page
show,DESeqResults-method Man page
sizeFactors Man page Man page
sizeFactors,DESeqDataSet-method Man page
sizeFactors.DESeqDataSet Source code
sizeFactors<-,DESeqDataSet,numeric-method Man page
sparseTest Source code
summary Man page
summary.DESeqResults Man page Source code
trimmedCellVariance Source code
trimmedVariance Source code
unmix Man page Source code
varianceStabilizingTransformation Man page Source code
vst Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllClasses.R
R/AllGenerics.R
R/RcppExports.R
R/core.R
R/expanded.R
R/fitNbinomGLMs.R
R/helper.R
R/methods.R
R/plots.R
R/results.R
R/rlog.R
R/vst.R
R/wrappers.R
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/DESeq2.R
inst/doc/DESeq2.Rmd
inst/doc/DESeq2.html
inst/script
inst/script/makeSim.R
inst/script/runScripts.R
inst/script/simulateCluster.R
inst/script/simulateDE.R
inst/script/simulateLFCAccuracy.R
inst/script/simulateOutliers.R
inst/script/simulation.Rmd
inst/script/simulation.pdf
inst/script/testsuite.Rmd
inst/script/vst.nb
inst/script/vst.pdf
man
man/DESeq.Rd
man/DESeq2-package.Rd
man/DESeqDataSet.Rd
man/DESeqResults.Rd
man/DESeqTransform.Rd
man/coef.Rd
man/collapseReplicates.Rd
man/counts.Rd
man/design.Rd
man/dispersionFunction.Rd
man/dispersions.Rd
man/estimateBetaPriorVar.Rd
man/estimateDispersions.Rd
man/estimateDispersionsGeneEst.Rd
man/estimateSizeFactors.Rd
man/estimateSizeFactorsForMatrix.Rd
man/fpkm.Rd
man/fpm.Rd
man/lfcShrink.Rd
man/makeExampleDESeqDataSet.Rd
man/nbinomLRT.Rd
man/nbinomWaldTest.Rd
man/normTransform.Rd
man/normalizationFactors.Rd
man/normalizeGeneLength.Rd
man/plotCounts.Rd
man/plotDispEsts.Rd
man/plotMA.Rd
man/plotPCA.Rd
man/plotSparsity.Rd
man/replaceOutliers.Rd
man/results.Rd
man/rlog.Rd
man/show.Rd
man/sizeFactors.Rd
man/summary.Rd
man/unmix.Rd
man/varianceStabilizingTransformation.Rd
man/vst.Rd
src
src/DESeq2.cpp
src/Makevars
src/Makevars.win
src/RcppExports.cpp
tests
tests/testthat
tests/testthat.R
tests/testthat/test_1vs1.R
tests/testthat/test_DESeq.R
tests/testthat/test_LRT.R
tests/testthat/test_QR.R
tests/testthat/test_addMLE.R
tests/testthat/test_betaFitting.R
tests/testthat/test_collapse.R
tests/testthat/test_construction_errors.R
tests/testthat/test_counts_input.R
tests/testthat/test_custom_filt.R
tests/testthat/test_disp_fit.R
tests/testthat/test_dispersions.R
tests/testthat/test_edge_case.R
tests/testthat/test_factors.R
tests/testthat/test_fpkm.R
tests/testthat/test_frozen_transform.R
tests/testthat/test_htseq.R
tests/testthat/test_interactions.R
tests/testthat/test_lfcShrink.R
tests/testthat/test_linear_mu.R
tests/testthat/test_methods.R
tests/testthat/test_model_matrix.R
tests/testthat/test_nbinomWald.R
tests/testthat/test_optim.R
tests/testthat/test_outlier.R
tests/testthat/test_parallel.R
tests/testthat/test_plots.R
tests/testthat/test_results.R
tests/testthat/test_rlog.R
tests/testthat/test_size_factor.R
tests/testthat/test_tximport.R
tests/testthat/test_unmix_samples.R
tests/testthat/test_vst.R
tests/testthat/test_weights.R
vignettes
vignettes/DESeq2.Rmd
vignettes/library.bib
vignettes/sed_call
DESeq2 documentation built on May 20, 2017, 9:35 p.m.

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