DESeq2
This is the development version of DESeq2; for the stable release version, see DESeq2.
Differential gene expression analysis based on the negative binomial distribution
Bioconductor version: Development (3.23)
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 [aut, cre], Constantin Ahlmann-Eltze [ctb], Kwame Forbes [ctb], Simon Anders [aut, ctb], Wolfgang Huber [aut, ctb], RADIANT EU FP7 [fnd], NIH NHGRI [fnd], CZI [fnd]
Maintainer: Michael Love <michaelisaiahlove at gmail.com>
citation("DESeq2")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("DESeq2")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | Bayesian, ChIPSeq, Clustering, DifferentialExpression, GeneExpression, ImmunoOncology, Normalization, PrincipalComponent, RNASeq, Regression, Sequencing, Software, Transcription |
| Version | 1.51.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (12.5 years) |
| License | LGPL (>= 3) |
| Depends | S4Vectors(>= 0.23.18), IRanges, GenomicRanges, SummarizedExperiment(>= 1.1.6) |
| Imports | BiocGenerics(>= 0.7.5), Biobase, BiocParallel, matrixStats, methods, stats4, locfit, ggplot2 (>= 3.4.0), Rcpp (>= 0.11.0), MatrixGenerics |
| System Requirements | |
| URL | https://github.com/thelovelab/DESeq2 |
See More
| Suggests | testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer, apeglm, ashr, tximport, tximeta, tximportData, readr, pbapply, airway, glmGamPoi, BiocManager |
| Linking To | Rcpp, RcppArmadillo |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |