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

Files in this package

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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