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

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
Date of publicationNone
MaintainerMichael Love <michaelisaiahlove@gmail.com>
LicenseLGPL (>= 3)
Version1.14.1

View on Bioconductor

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

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 on log scale

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

varianceStabilizingTransformation: Apply a variance stabilizing transformation (VST) to the...

vst: Quickly estimate dispersion trend and apply a variance...

Functions

coef Man page
coef.DESeqDataSet Man page
collapseReplicates Man page
counts Man page
counts<-,DESeqDataSet,matrix-method Man page
counts,DESeqDataSet-method Man page
DESeq Man page
DESeq2-package Man page
DESeqDataSet Man page
DESeqDataSet-class Man page
DESeqDataSetFromHTSeqCount Man page
DESeqDataSetFromMatrix Man page
DESeqDataSetFromTximport Man page
DESeqResults Man page
DESeqResults-class Man page
DESeqTransform Man page
DESeqTransform-class Man page
design Man page
design<-,DESeqDataSet,formula-method Man page
design,DESeqDataSet-method Man page
dispersionFunction Man page
dispersionFunction<- Man page
dispersionFunction<-,DESeqDataSet,function-method Man page
dispersionFunction,DESeqDataSet-method Man page
dispersions Man page
dispersions<- Man page
dispersions,DESeqDataSet-method Man page
dispersions<-,DESeqDataSet,numeric-method Man page
estimateBetaPriorVar Man page
estimateDispersions Man page
estimateDispersions,DESeqDataSet-method Man page
estimateDispersionsFit Man page
estimateDispersionsGeneEst Man page
estimateDispersionsMAP Man page
estimateDispersionsPriorVar Man page
estimateMLEForBetaPriorVar Man page
estimateSizeFactors Man page
estimateSizeFactors,DESeqDataSet-method Man page
estimateSizeFactorsForMatrix Man page
fpkm Man page
fpm Man page
getVarianceStabilizedData Man page
makeExampleDESeqDataSet Man page
nbinomLRT Man page
nbinomWaldTest Man page
normalizationFactors Man page
normalizationFactors<- Man page
normalizationFactors<-,DESeqDataSet,matrix-method Man page
normalizationFactors,DESeqDataSet-method Man page
normalizeGeneLength Man page
normTransform Man page
plotCounts Man page
plotDispEsts Man page
plotDispEsts,DESeqDataSet-method Man page
plotMA Man page
plotMA,DESeqDataSet-method Man page
plotMA,DESeqResults-method Man page
plotPCA Man page
plotPCA,DESeqTransform-method Man page
plotSparsity Man page
removeResults Man page
replaceOutliers Man page
replaceOutliersWithTrimmedMean Man page
results Man page
resultsNames Man page
rlog Man page
rlogTransformation Man page
show Man page
show,DESeqResults-method Man page
sizeFactors Man page
sizeFactors,DESeqDataSet-method Man page
sizeFactors<-,DESeqDataSet,numeric-method Man page
summary Man page
summary.DESeqResults Man page
varianceStabilizingTransformation Man page
vst Man page

Files

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

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