Mercurial > repos > yhoogstrate > edger_with_design_matrix
diff edgeR_Differential_Gene_Expression.xml @ 79:c86f1f86b3c1 draft
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| author | yhoogstrate |
|---|---|
| date | Thu, 13 Nov 2014 10:30:43 -0500 |
| parents | 2ee2336d71cc |
| children | b2738b4d7c8c |
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--- a/edgeR_Differential_Gene_Expression.xml Tue Sep 30 11:29:52 2014 -0400 +++ b/edgeR_Differential_Gene_Expression.xml Thu Nov 13 10:30:43 2014 -0500 @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="edger_dge" name="edgeR: Differential Gene(Expression) Analysis"> +<tool id="edger_dge" name="edgeR: Differential Gene(Expression) Analysis" version="3.0.3-latest.a"> <description>RNA-Seq gene expression analysis using edgeR (R package)</description> <requirements> @@ -10,6 +10,8 @@ <requirement type="package" version="1.3.18">graphicsmagick</requirement> </requirements> + <version_command>R --vanilla --slave -e "library(edgeR) ; cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null</version_command> + <command> <!-- The following script is written in the "Cheetah" language: @@ -512,7 +514,7 @@ the correct contrast ( http://en.wikipedia.org/wiki/Contrast_(statistics) ) has to be given. If you have for example two groups, with an equal weight, you would like to compare either -"g1~g2" or "normal~cancer". +"g1-g2" or "normal-cancer". The test function makes use of a MCF7 dataset used in a study that indicates that a higher sequencing depth is not neccesairily more important than a higher amount of replaciates[2]. @@ -566,18 +568,17 @@ - R - Bioconductor - - limma - - - edgeR + - limma + - edgeR License ------- - R - - GPL-2 & GPL-3 + - GPL 2 & GPL 3 - limma - GPL (>=2) - edgeR - - GPL (>=2) + - GPL (>=2) References ---------- @@ -603,12 +604,18 @@ Contact ------- -The tool wrapper has been written by Youri Hoogstrate from the Erasmus Medical Center (Rotterdam, Netherlands) on behalf of the Translational Research IT (TraIT) project: + +The tool wrapper has been written by Youri Hoogstrate from the Erasmus +Medical Center (Rotterdam, Netherlands) on behalf of the Translational +Research IT (TraIT) project: http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch +More tools by the Translational Research IT (TraIT) project can be found +in the following toolsheds: +- http://toolshed.dtls.nl/ +- http://toolshed.g2.bx.psu.edu +- http://testtoolshed.g2.bx.psu.edu/ + I would like to thank Hina Riaz - Naz Khan for her helpful contribution. - -More tools by the Translational Research IT (TraIT) project can be found in the following repository: -http://testtoolshed.g2.bx.psu.edu/ </help> </tool>