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Provides an integrated solution for analysing data from gene expression experiments. limma contains rich features for handling complex experimental designs and for information borrowing to overcome the problem of small sample sizes. It also contains particularly strong facilities for reading, normalizing and exploring such data. Recently, the capabilities of limma have been significantly expanded in two important directions: (i) it can perform both differential expression and differential splicing analyses of RNA-seq data; (ii) the package is now able to go past the traditional gene-wise expression analyses in a variety of ways, analysing expression profiles in terms of co-regulated sets of genes or in terms of higher-order expression signatures. This provides enhanced possibilities for biological interpretation of gene expression differences.

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limma specifications

Software type:
Package
Restrictions to use:
None
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU General Public License version 2.0
Version:
3.24.15
Requirements:
R, methods

Publications

  • (Smyth et al., 2005) Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics.
    Published on: 2005 May 01
    PMID: 15657102

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Documentation

Maintainer

Credits

Institution(s)

Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia

Funding source(s)

National Health and Medical Research Council Project Grant [1050661 and 1023454]; NHMRC Program Grant [1054618]; Victorian State Government Operational Infrastructure Support and Australian Government NHMRC IRIISS

Link to literature

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