DESeq2
This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see DESeq2.
Differential gene expression analysis based on the negative binomial distribution
Bioconductor version: 3.6
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
Maintainer: Michael Love <michaelisaiahlove at gmail.com>
Citation (from within R, enter
citation("DESeq2")):
Installation
To install this package, start R (version "3.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DESeq2")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | ChIPSeq, DifferentialExpression, GeneExpression, RNASeq, SAGE, Sequencing, Software, Transcription |
| Version | 1.18.1 |
| In Bioconductor since | BioC 2.12 (R-3.0) (11 years) |
| License | LGPL (>= 3) |
| Depends | S4Vectors(>= 0.9.25), IRanges, GenomicRanges, SummarizedExperiment(>= 1.1.6) |
| Imports | BiocGenerics(>= 0.7.5), Biobase, BiocParallel, genefilter, methods, locfit, geneplotter, ggplot2, Hmisc, Rcpp (>= 0.11.0) |
| System Requirements | |
| URL | https://github.com/mikelove/DESeq2 |
See More
| Suggests | testthat, knitr, BiocStyle, vsn, pheatmap, RColorBrewer, IHW, apeglm, ashr, tximport, tximportData, readr, pbapply, airway, pasilla(>= 0.2.10) |
| Linking To | Rcpp, RcppArmadillo |
| Enhances | |
| Depends On Me | DChIPRep, DEXSeq, FourCSeq, MLSeq, rgsepd, TCC, XBSeq |
| Imports Me | anamiR, Anaquin, anota2seq, coseq, DaMiRseq, debrowser, DEFormats, DEGreport, DEsubs, DiffBind, eegc, EnrichmentBrowser, FourCSeq, GenoGAM, HTSFilter, ideal, IHWpaper, ImpulseDE2, IntEREst, isomiRs, JunctionSeq, PathoStat, pcaExplorer, regionReport, ReportingTools, SNPhood, systemPipeR, ToPASeq |
| Suggests Me | apeglm, biobroom, BiocGenerics, BioCor, compcodeR, DASC, derfinder, diffloop, gage, GenomicAlignments, GenomicRanges, Glimma, IHW, JctSeqData, miRmine, oneChannelGUI, OPWeight, phyloseq, progeny, recount, RUVSeq, scran, Single.mTEC.Transcriptomes, subSeq, tximport, variancePartition |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DESeq2_1.18.1.tar.gz |
| Windows Binary | DESeq2_1.18.1.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | DESeq2_1.18.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DESeq2 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DESeq2 |
| Package Short Url | https://bioconductor.org/packages/DESeq2/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.6 | Source Archive |