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

Author
Simon Anders, EMBL Heidelberg <sanders@fs.tum.de>
Date of publication
None
Maintainer
Simon Anders <sanders@fs.tum.de>
License
GPL (>= 3)
Version
1.26.0
URLs

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