comparison edgeR_Differential_Gene_Expression.xml @ 79:c86f1f86b3c1 draft

Uploaded

78:398963a4827a

<?xml version="1.0" encoding="UTF-8"?>
<tool id="edger_dge" name="edgeR: Differential Gene(Expression) Analysis">
	<description>RNA-Seq gene expression analysis using edgeR (R package)</description>
	
	<requirements>
		<!--<requirement type="package" version="3.0.1">package_r3_withx</requirement>-->
		<!--<requirement type="package" version="3.1.0">R</requirement>-->
		<requirement type="package" version="3.0.3">R</requirement>
		<requirement type="package" version="latest">biocLite_edgeR_limma</requirement>
		<requirement type="package" version="1.3.18">graphicsmagick</requirement>
	</requirements>
	
	<command>
		<!--
			The following script is written in the "Cheetah" language:
			http://www.cheetahtemplate.org/docs/users_guide_html_multipage/contents.html

This tool is called *edgeR Design Matrix Creator*.
If the appropriate design matrix (with corresponding links to the files) is given,
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".

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].

Input
-----

This tool requires no specific configurations. The following dependencies are installed automatically:

- R
- Bioconductor
   - limma

   - edgeR

License
-------
- R
   - GPL-2 & GPL-3
- limma
    - GPL (>=2)
- edgeR
     - GPL (>=2)

References
----------

EdgeR

- http://www.ncbi.nlm.nih.gov/pubmed/24319002
- http://dx.doi.org/10.1093/bioinformatics/btt688

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:
http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch

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>

79:c86f1f86b3c1

<?xml version="1.0" encoding="UTF-8"?>
<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>
		<!--<requirement type="package" version="3.0.1">package_r3_withx</requirement>-->
		<!--<requirement type="package" version="3.1.0">R</requirement>-->
		<requirement type="package" version="3.0.3">R</requirement>
		<requirement type="package" version="latest">biocLite_edgeR_limma</requirement>
		<requirement type="package" version="1.3.18">graphicsmagick</requirement>
	</requirements>
	
	<version_command>R --vanilla --slave -e "library(edgeR) ; cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2&gt; /dev/null</version_command>
	
	<command>
		<!--
			The following script is written in the "Cheetah" language:
			http://www.cheetahtemplate.org/docs/users_guide_html_multipage/contents.html

This tool is called *edgeR Design Matrix Creator*.
If the appropriate design matrix (with corresponding links to the files) is given,
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".

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].

Input
-----

This tool requires no specific configurations. The following dependencies are installed automatically:

- R
- Bioconductor
    - limma
    - edgeR

License
-------
- R
    - GPL 2 & GPL 3
- limma
    - GPL (>=2)
- edgeR
    - GPL (>=2)

References
----------

EdgeR

- http://www.ncbi.nlm.nih.gov/pubmed/24319002
- http://dx.doi.org/10.1093/bioinformatics/btt688

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:
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.
	</help>
</tool>