DESeq2 v1.12.3

by Michael Love

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.

Functions in DESeq2

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


Type Package
License LGPL (>= 3)
VignetteBuilder knitr
LinkingTo Rcpp, RcppArmadillo
biocViews Sequencing, ChIPSeq, RNASeq, SAGE, DifferentialExpression, GeneExpression, Transcription
RoxygenNote 5.0.1

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