DESeq: 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

AuthorSimon Anders, EMBL Heidelberg <sanders@fs.tum.de>
Date of publicationNone
MaintainerSimon Anders <sanders@fs.tum.de>
LicenseGPL (>= 3)
Version1.26.0
http://www-huber.embl.de/users/anders/DESeq

View on Bioconductor

Man pages

adjustScvForBias: Adjust an SCV value for the bias arising when it is...

conditions: Accessor functions for the 'conditions' information in a...

CountDataSet-class: Class "CountDataSet" - a container for count data from HTS...

counts: Accessors for the 'counts' slot of a CountDataSet object.

dispTable: Accessor function for the dispTable information in a...

estimateDispersions: Estimate and fit dispersions for a CountDataSet.

estimateSizeFactors: Estimate the size factors for a CountDataSet

estimateSizeFactorsForMatrix: Low-level function to estimate size factors with robust...

estimateVarianceFunctions: REMOVED

fitInfo: Accessor function for the fitInfo objects in a CountDataSet

fitNbinomGLMs: Fit a generalized linear model (GLM) for each gene.

fitNbinomGLMsForMatrix: Fit negative binomial GLMs to a count matrix.

getBaseMeansAndVariances: Perform row-wise estimates of base-level means and variances...

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

makeExampleCountDataSet: make a simple example CountDataSet with random data

nbinomGLMTest: Perform chi-squared tests comparing two sets of GLM fits

nbinomTest: Test for differences between the base means for two...

nbinomTestForMatrices: Perform row-wise tests for differences between the base means...

nbkd.sf: GLM family for a negative binomial with known dispersion and...

newCountDataSet: Create a CountDataSet object

newCountDataSetFromHTSeqCount: Create a new CountDataSet from count files generated with...

plotDispEsts: Plot dispersion estimates and fitted values

plotMA: Makes a so-called "MA-plot"

plotPCA: Sample PCA plot from variance-stabilized data

residualsEcdfPlot: REMOVED

scvPlot: REMOVED

sizeFactors: Accessor functions for the 'sizeFactors' information in a...

varianceFitDiagnostics: REMOVED

Functions

adjustScvForBias Man page
conditions Man page
conditions<-,CountDataSet-method Man page
conditions,CountDataSet-method Man page
CountDataSet-class Man page
counts Man page
counts<-,CountDataSet,matrix-method Man page
counts,CountDataSet-method Man page
dispTable Man page
dispTable,CountDataSet-method Man page
estimateDispersions Man page
estimateDispersions,CountDataSet-method Man page
estimateSizeFactors Man page
estimateSizeFactors,CountDataSet-method Man page
estimateSizeFactorsForMatrix Man page
estimateVarianceFunctions Man page
fitInfo Man page
fitNbinomGLMs Man page
fitNbinomGLMsForMatrix Man page
getBaseMeansAndVariances Man page
getVarianceStabilizedData Man page
makeExampleCountDataSet Man page
nbinomGLMTest Man page
nbinomTest Man page
nbinomTestForMatrices Man page
nbkd.sf Man page
newCountDataSet Man page
newCountDataSetFromHTSeqCount Man page
plotDispEsts Man page
plotMA Man page
plotPCA Man page
residualsEcdfPlot Man page
scvPlot Man page
sizeFactors Man page
sizeFactors,CountDataSet-method Man page
sizeFactors<-,CountDataSet,numeric-method Man page
varianceFitDiagnostics Man page
varianceStabilizingTransformation Man page

Files

DESeq/DESCRIPTION
DESeq/NAMESPACE
DESeq/NEWS
DESeq/R
DESeq/R/class_and_slots.R DESeq/R/core.R DESeq/R/methods.R DESeq/R/plotDispEsts.R DESeq/R/welcome.R
DESeq/build
DESeq/build/vignette.rds
DESeq/inst
DESeq/inst/CITATION
DESeq/inst/doc
DESeq/inst/doc/DESeq.R
DESeq/inst/doc/DESeq.Rnw
DESeq/inst/doc/DESeq.pdf
DESeq/inst/extra
DESeq/inst/extra/TagSeqExample.tab
DESeq/inst/extra/scvBiasCorrectionFits.rda
DESeq/inst/scripts
DESeq/inst/scripts/testVarianceStabilizingTransformation.R
DESeq/man
DESeq/man/CountDataSet-class.Rd DESeq/man/adjustScvForBias.Rd DESeq/man/conditions.Rd DESeq/man/counts.Rd DESeq/man/dispTable.Rd DESeq/man/estimateDispersions.Rd DESeq/man/estimateSizeFactors.Rd DESeq/man/estimateSizeFactorsForMatrix.Rd DESeq/man/estimateVarianceFunctions.Rd DESeq/man/fitInfo.Rd DESeq/man/fitNbinomGLMs.Rd DESeq/man/fitNbinomGLMsForMatrix.Rd DESeq/man/getBaseMeansAndVariances.Rd DESeq/man/getVarianceStabilizedData.Rd DESeq/man/makeExampleCountDataSet.Rd DESeq/man/nbinomGLMTest.Rd DESeq/man/nbinomTest.Rd DESeq/man/nbinomTestForMatrices.Rd DESeq/man/nbkd.sf.Rd DESeq/man/newCountDataSet.Rd DESeq/man/newCountDataSetFromHTSeqCount.Rd DESeq/man/plotDispEsts.Rd DESeq/man/plotMA.Rd DESeq/man/plotPCA.Rd DESeq/man/residualsEcdfPlot.Rd DESeq/man/scvPlot.Rd DESeq/man/sizeFactors.Rd DESeq/man/varianceFitDiagnostics.Rd
DESeq/src
DESeq/src/pval.c
DESeq/vignettes
DESeq/vignettes/DESeq.Rnw
DESeq/vignettes/DESeq.bib
DESeq/vignettes/vst.nb
DESeq/vignettes/vst.pdf
DESeq/vignettes/whbiocvignette.sty

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