limma

The limma (limma-voom) tool is for the analysis of gene expression of microarray and RNA-seq data. The limma algorithm uses a generalized linear model (GLM), log-normal distribution, trimmed mean of M-values, t- and F-tests.

Topic

Sequencing;RNA-Seq

Detail

  • Operation: RNA-Seq analysis;Differential gene expression analysis

  • Software interface: Command-line user interface;Library

  • Language: R

  • License: GNU General Public License v>=2

  • Cost: Free

  • Version name: 3.58.1

  • Credit: National Health and Medical Research Council (NHMRC), Victorian State Government Operational Infrastructure Support and Australian Government NHMRC IRIISS.

  • Input: -

  • Output: -

  • Contact: Gordon Smyth smyth@wehi.edu.au

  • Collection: Bioconductor

  • Maturity: Mature

Publications

  • limma powers differential expression analyses for RNA-sequencing and microarray studies.
  • Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015 Apr 20;43(7):e47. doi: 10.1093/nar/gkv007. Epub 2015 Jan 20. PMID: 25605792; PMCID: PMC4402510.
  • https://doi.org/10.1093/nar/gkv007
  • PMID: 25605792
  • PMC: PMC4402510
  • voom: Precision weights unlock linear model analysis tools for RNA-seq read counts.
  • Law CW, et al. voom: Precision weights unlock linear model analysis tools for RNA-seq read counts. voom: Precision weights unlock linear model analysis tools for RNA-seq read counts. 2014; 15:R29. doi: 10.1186/gb-2014-15-2-r29
  • https://doi.org/10.1186/gb-2014-15-2-r29
  • PMID: 24485249
  • PMC: PMC4053721

Download and documentation

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