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.

AuthorMichael Love, Simon Anders, Wolfgang Huber
Date of publicationNone
MaintainerMichael Love <michaelisaiahlove@gmail.com>
LicenseLGPL (>= 3)
Version1.14.1

View on Bioconductor

Man pages

coef: Extract a matrix of model coefficients/standard errors

collapseReplicates: Collapse technical replicates in a RangedSummarizedExperiment...

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

DESeq: Differential expression analysis based on the Negative...

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

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

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

dispersions: Accessor functions for the dispersion estimates in a...

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...

fpkm: FPKM: fragments per kilobase per million mapped fragments

fpm: FPM: fragments per million mapped fragments

makeExampleDESeqDataSet: Make a simulated DESeqDataSet

nbinomLRT: Likelihood ratio test (chi-squared test) for GLMs

nbinomWaldTest: Wald test for the GLM coefficients

normalizationFactors: Accessor functions for the normalization factors in a...

normalizeGeneLength: Normalize for gene length

normTransform: Normalized counts transformation

plotCounts: Plot of normalized counts for a single gene on log scale

plotDispEsts: Plot dispersion estimates

plotMA: MA-plot from base means and log fold changes

plotPCA: Sample PCA plot for transformed data

plotSparsity: Sparsity plot

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...

summary: Summarize DESeq results

varianceStabilizingTransformation: Apply a variance stabilizing transformation (VST) to the...

vst: Quickly estimate dispersion trend and apply a variance...

Files in this package

DESeq2/DESCRIPTION
DESeq2/NAMESPACE
DESeq2/NEWS
DESeq2/R
DESeq2/R/AllClasses.R DESeq2/R/AllGenerics.R DESeq2/R/RcppExports.R DESeq2/R/core.R DESeq2/R/expanded.R DESeq2/R/helper.R DESeq2/R/methods.R DESeq2/R/plots.R DESeq2/R/results.R DESeq2/R/rlog.R DESeq2/R/vst.R
DESeq2/build
DESeq2/build/vignette.rds
DESeq2/inst
DESeq2/inst/CITATION
DESeq2/inst/doc
DESeq2/inst/doc/DESeq2.R
DESeq2/inst/doc/DESeq2.Rnw
DESeq2/inst/doc/DESeq2.pdf
DESeq2/inst/script
DESeq2/inst/script/makeSim.R
DESeq2/inst/script/runScripts.R
DESeq2/inst/script/simulateCluster.R
DESeq2/inst/script/simulateDE.R
DESeq2/inst/script/simulateLFCAccuracy.R
DESeq2/inst/script/simulateOutliers.R
DESeq2/inst/script/simulation.Rmd
DESeq2/inst/script/simulation.pdf
DESeq2/inst/script/testsuite.Rmd
DESeq2/inst/script/vst.nb
DESeq2/inst/script/vst.pdf
DESeq2/man
DESeq2/man/DESeq.Rd DESeq2/man/DESeq2-package.Rd DESeq2/man/DESeqDataSet.Rd DESeq2/man/DESeqResults.Rd DESeq2/man/DESeqTransform.Rd DESeq2/man/coef.Rd DESeq2/man/collapseReplicates.Rd DESeq2/man/counts.Rd DESeq2/man/design.Rd DESeq2/man/dispersionFunction.Rd DESeq2/man/dispersions.Rd DESeq2/man/estimateBetaPriorVar.Rd DESeq2/man/estimateDispersions.Rd DESeq2/man/estimateDispersionsGeneEst.Rd DESeq2/man/estimateSizeFactors.Rd DESeq2/man/estimateSizeFactorsForMatrix.Rd DESeq2/man/fpkm.Rd DESeq2/man/fpm.Rd DESeq2/man/makeExampleDESeqDataSet.Rd DESeq2/man/nbinomLRT.Rd DESeq2/man/nbinomWaldTest.Rd DESeq2/man/normTransform.Rd DESeq2/man/normalizationFactors.Rd DESeq2/man/normalizeGeneLength.Rd DESeq2/man/plotCounts.Rd DESeq2/man/plotDispEsts.Rd DESeq2/man/plotMA.Rd DESeq2/man/plotPCA.Rd DESeq2/man/plotSparsity.Rd DESeq2/man/replaceOutliers.Rd DESeq2/man/results.Rd DESeq2/man/rlog.Rd DESeq2/man/show.Rd DESeq2/man/sizeFactors.Rd DESeq2/man/summary.Rd DESeq2/man/varianceStabilizingTransformation.Rd DESeq2/man/vst.Rd
DESeq2/src
DESeq2/src/DESeq2.cpp
DESeq2/src/Makevars
DESeq2/src/Makevars.win
DESeq2/src/RcppExports.cpp
DESeq2/tests
DESeq2/tests/testthat
DESeq2/tests/testthat.R
DESeq2/tests/testthat/test_1vs1.R
DESeq2/tests/testthat/test_DESeq.R
DESeq2/tests/testthat/test_LRT.R
DESeq2/tests/testthat/test_LRT_prior.R
DESeq2/tests/testthat/test_QR.R
DESeq2/tests/testthat/test_addMLE.R
DESeq2/tests/testthat/test_betaFitting.R
DESeq2/tests/testthat/test_collapse.R
DESeq2/tests/testthat/test_construction_errors.R
DESeq2/tests/testthat/test_counts_input.R
DESeq2/tests/testthat/test_custom_filt.R
DESeq2/tests/testthat/test_disp_fit.R
DESeq2/tests/testthat/test_dispersions.R
DESeq2/tests/testthat/test_edge_case.R
DESeq2/tests/testthat/test_factors.R
DESeq2/tests/testthat/test_fpkm.R
DESeq2/tests/testthat/test_frozen_transform.R
DESeq2/tests/testthat/test_htseq.R
DESeq2/tests/testthat/test_interactions.R
DESeq2/tests/testthat/test_linear_mu.R
DESeq2/tests/testthat/test_methods.R
DESeq2/tests/testthat/test_model_matrix.R
DESeq2/tests/testthat/test_nbinomWald.R
DESeq2/tests/testthat/test_optim.R
DESeq2/tests/testthat/test_outlier.R
DESeq2/tests/testthat/test_parallel.R
DESeq2/tests/testthat/test_plots.R
DESeq2/tests/testthat/test_results.R
DESeq2/tests/testthat/test_rlog.R
DESeq2/tests/testthat/test_size_factor.R
DESeq2/tests/testthat/test_tximport.R
DESeq2/tests/testthat/test_vst.R
DESeq2/tests/testthat/test_zero_zero.R
DESeq2/vignettes
DESeq2/vignettes/DESeq2.Rnw
DESeq2/vignettes/library.bib

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