DESeq2

DESeq2 is a software package for the differential analysis of count data obtained from comparative high-throughput sequencing experiments, such as RNA-seq. It addresses the unique challenges these datasets pose, including small sample sizes, discrete counts, wide dynamic ranges, and outliers.

The key features of DESeq2 include:

1. Improved stability and interpretability of estimates through shrinkage estimation for dispersion and fold change calculations.

2. A focus on the quantitative analysis of differential expression, allowing researchers to assess the magnitude of changes rather than just their presence or absence.

3. Seamless integration with the Bioconductor platform, a widely used open-source software project for analyzing and comprehending high-throughput genomic data.

Topic

Transcriptomics

Detail

  • Operation: Differential gene expression analysis

  • Software interface: Command-line user interface

  • Language: R

  • License: GNU Lesser General Public License, version 2.1

  • Cost: Free

  • Version name: 1.44.0

  • Credit: The International Max Planck Research School for Computational Biology and Scientific Computing, the National Institutes of Health, the European Union’s 7th Framework Programme (Health) via Project Radiant.

  • Input: -

  • Output: -

  • Contact: Michael Love michaelisaiahlove@gmail.com

  • Collection: -

  • Maturity: Mature

Publications

  • Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
  • Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. doi: 10.1186/s13059-014-0550-8. PMID: 25516281; PMCID: PMC4302049.
  • https://doi.org/10.1186/s13059-014-0550-8
  • PMID: 25516281
  • PMC: PMC4302049

Download and documentation

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