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<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<meta name="DESCRIPTION" content="Software authored by Gordon Smyth">
<meta name="viewport" content="width=device-width, initial-scale=1">
<link rel="stylesheet" type="text/css" href="res.css">
<title>Gordon Smyth: Software</title>
<link rel="canonical" href="https://gksmyth.github.io/software.html">
</head>
<body bgcolor="#FFFFFF" text="#000000" link="#000FFF">
<p class="parent">
<a href="index.html">Gordon Smyth Home</a></p>
<h1>Software</h1>
<hr>
<h2>Bioconductor R packages</h2>
<p><a href="http://bioinf.wehi.edu.au/limma">limma</a> (2002–present) has extensive capabilities for pre-processing and differential expression analysis of microarray and RNA-seq experiments.</p>
<p>
News: <a href="eurekaprize.html"><b>limma wins 2024 Eureka Prize for Excellence in Research Software!</b></a>
</p>
<p><a href="https://doi.org/doi:10.18129/B9.bioc.limpa">limpa</a> (2025–present) performs quantification and differential analysis of mass-spectrometry proteomics data, with probabilistic recovery of information from missing values.
</p>
<p><a href="https://doi.org/doi:10.18129/B9.bioc.edgeR">edgeR</a> (2008–present) performs differential analysis of omics data based on sequence read counts, including RNA-Seq, ChIP-Seq, ATAC-seq, Hi-C etc. Is able to separate technical from biological variation and to borrow strength between transcripts or tags.</p>
<p><a href="https://doi.org/doi:10.18129/B9.bioc.goseq">goseq</a> (2009–present) provides functional analysis of gene lists from RNA-Seq experiments, adjusting for gene length bias. Authored by Matt Young and maintained by Nadia Davidson.</p>
<p><a href="https://doi.org/doi:10.18129/B9.bioc.csaw">csaw</a> (2014–present) performs differential binding analyses of ChIP-seq experiments.
Developed and maintained by Aaron Lun.
See the Bioconductor Newsletter article on <a href="http://www.bioconductor.org/help/newsletters/2015_January/#overview-of-the-csaw-package">An overview of the csaw package</a>.
</p>
<p><a href="https://doi.org/doi:10.18129/B9.bioc.diffHic">diffHic</a> (2015–present) performs differential interaction analyses of Hi-C experiments.
Developed and maintained by Aaron Lun.
</p>
<p><a href="https://doi.org/doi:10.18129/B9.bioc.limmaGUI">limmaGUI</a> (2003–present) provides a menu-driven interface to the limma package for analysing two-colour microarray data [41].
Developed by James Wettenhall and maintained by me.</p>
<p><a href="https://doi.org/doi:10.18129/B9.bioc.affylmGUI">affylmGUI</a> (2004–present) provides a menu-driven interface to the affy, gcrma, affyPLM and limma packages for analysing Affymetrix microarray data [49].
Developed by James Wettenhall and maintained by me.</p>
<h2>CRAN R packages</h2>
<p><a href="http://cran.r-project.org/web/packages/statmod/index.html">statmod</a> (2001–present). An R package for biostatistical modelling, including REML analyses, Tweedie generalized linear models, comparative growth curve analysis, and limiting dilution analyses.</p>
<p><a href="http://cran.r-project.org/web/packages/dglm/index.html">dglm</a>. Double generalized linear models.</p>
<p><a href="http://cran.r-project.org/web/packages/tweedie/index.html">tweedie</a>. Functions for Tweedie distributions, exponential family distributions with power-variance functions. Maintained by Peter Dunn.</p>
<h2>Web tools</h2>
<p><a href="http://bioinf.wehi.edu.au/software/elda">ELDA</a>. Extreme limiting dilution analysis for comparing stem cell frequencies between populations.</p>
<p><a href="http://bioinf.wehi.edu.au/software/compareCurves">Compare Growth Curves</a>. Permutation test for comparing groups of growth curves.</p>
<h2>S-Plus</h2>
I have authored a wide variety <a href="s/index.html">statistical modelling functions for S-Plus</a>, although I no longer maintain these.
<h2>Matlab</h2>
<p><a href="matlab/index.html">statbox</a> (1990–2001) is a statistics toolbox for Matlab, including ordinal logistic regression and linear mixed models.
No longer maintained.</p>
<p> </p>
<hr>
<p> </p>
</body></html>