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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.

Functions (41)

DESeq

Differential expression analysis based on the Negative Binomial (a.k.a. Gamma-Poisson) distribution

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

coef

Extract a matrix of model coefficients/standard errors

collapseReplicates

Collapse technical replicates in a RangedSummarizedExperiment or DESeqDataSet

counts

Accessors for the 'counts' slot of a DESeqDataSet object.

design

Accessors for the 'design' slot of a DESeqDataSet object.

dispersionFunction

Accessors for the 'dispersionFunction' slot of a DESeqDataSet object.

dispersions

Accessor functions for the dispersion estimates in a DESeqDataSet object.

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 regression.

fpkm

FPKM: fragments per kilobase per million mapped fragments

fpm

FPM: fragments per million mapped fragments

integrateWithSingleCell

Integrate bulk DE results with Bioconductor single-cell RNA-seq datasets

lfcShrink

Shrink log2 fold changes

makeExampleDESeqDataSet

Make a simulated DESeqDataSet

nbinomLRT

Likelihood ratio test (chi-squared test) for GLMs

nbinomWaldTest

Wald test for the GLM coefficients

normTransform

Normalized counts transformation

normalizationFactors

Accessor functions for the normalization factors in a DESeqDataSet object.

normalizeGeneLength

Normalize for gene length

plotCounts

Plot of normalized counts for a single gene

plotDispEsts

Plot dispersion estimates

plotMA

MA-plot from base means and log fold changes

plotPCA

Sample PCA plot for transformed data

plotSparsity

Sparsity plot

priorInfo

Accessors for the 'priorInfo' slot of a DESeqResults object.

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 DESeqDataSet object.

summary

Summarize DESeq results

unmix

Unmix samples using loss in a variance stabilized space

varianceStabilizingTransformation

Apply a variance stabilizing transformation (VST) to the count data

vst

Quickly estimate dispersion trend and apply a variance stabilizing transformation

DESeq2

Differential gene expression analysis based on the negative binomial distribution

v1.30.1

LGPL (>= 3)

Authors

Michael Love [aut, cre], Constantin Ahlmann-Eltze [ctb], Kwame Forbes [ctb], Simon Anders [aut, ctb], Wolfgang Huber [aut, ctb]

Initial release

DESeq2

Functions (41)

DESeq2

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