DESeq2: Differential gene expression analysis based on the negative binomial distribution

Share:

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
Michael Love, Simon Anders, Wolfgang Huber
Date of publication
None
Maintainer
Michael Love <michaelisaiahlove@gmail.com>
License
LGPL (>= 3)
Version
1.14.1

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