Mercurial > repos > proteore > proteore_clusterprofiler
diff README.rst @ 0:bd052861852b draft
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author | proteore |
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date | Thu, 01 Mar 2018 10:05:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Thu Mar 01 10:05:18 2018 -0500 @@ -0,0 +1,45 @@ +Wrapper for clusterProfiler Enrichment Analysis Tool +==================================================== + +**Authors** + +clusterProfiler R package reference : +G Yu, LG Wang, Y Han, QY He. clusterProfiler: an R package for comparing biological themes among gene clusters. +OMICS: A Journal of Integrative Biology 2012, 16(5):284-287. +doi:[10.1089/omi.2011.0118](http://dx.doi.org/10.1089/omi.2011.0118) + + +**Galaxy integration** + +T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR + +Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform + +This work has been partially funded through the French National Agency for Research (ANR) IFB project. + +Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. + + +=================== + +**Galaxy component based on R package clusterProfiler (see ref below)** + +This component allows to perform GO enrichment-analyses. +Given a list of IDs, the tool either +(i) performs gene classification based on GO distribution at a specific level, or +(ii) calculates GO categories enrichment (over- or under-representation) for the IDs of the input list, +compared to a background (whole organism or user-defined list). + +**Input required** + +This component works with Gene ids (e.g : 4151, 7412) or Uniprot accession number (e.g. P31946). +You can copy/paste these identifiers or supply a tabular file (.csv, .tsv, .txt, .tab) where there are contained. + + +**Output** + +Text (tables) and graphics representing the repartition and/or enrichment of GO categories. + +**User manual / Documentation** of the clusterProfiler R package (functions and parameters): +https://bioconductor.org/packages/3.7/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html +(Very well explained) \ No newline at end of file