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DESeq2 (version 1.8.2)

Differential gene expression analysis based on the negative binomial distribution

Description

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.

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Version

Version

1.8.2

License

LGPL (>= 3)

Maintainer

Michael Love

Last Published

February 15th, 2017

Functions in DESeq2 (1.8.2)

DESeq2-package

DESeq2 package for differential analysis of count data
DESeqDataSet-class

DESeqDataSet object and constructors
estimateBetaPriorVar

Steps for estimating the beta prior variance
dispersions

Accessor functions for the dispersion estimates in a DESeqDataSet object.
results

Extract results from a DESeq analysis
replaceOutliers

Replace outliers with trimmed mean
sizeFactors

Accessor functions for the 'sizeFactors' information in a DESeqDataSet object.
summary

Summarize DESeq results
DESeqResults-class

DESeqResults object and constructor
DESeqTransform-class

DESeqTransform object and constructor
nbinomLRT

Likelihood ratio test (chi-squared test) for GLMs
nbinomWaldTest

Wald test for the GLM coefficients
show

Show method for DESeqResults objects
plotSparsity

Sparsity plot
rlog

Apply a 'regularized log' transformation
plotPCA

Sample PCA plot for transformed data
varianceStabilizingTransformation

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

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

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

FPM: fragments per million mapped fragments
counts

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

Low-level functions to fit dispersion estimates
DESeq

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

Make a simulated DESeqDataSet
estimateSizeFactors

Estimate the size factors for a DESeqDataSet
plotDispEsts

Plot dispersion estimates
plotMA

MA-plot from base means and log fold changes
coef

Extract a matrix of model coefficients/standard errors
collapseReplicates

Collapse technical replicates in a SummarizedExperiment or DESeqDataSet
estimateSizeFactorsForMatrix

Low-level function to estimate size factors with robust regression.
fpkm

FPKM: fragments per kilobase per million mapped fragments
normalizationFactors

Accessor functions for the normalization factors in a DESeqDataSet object.
plotCounts

Plot of normalized counts for a single gene on log scale