Mercurial > repos > proteore > proteore_clusterprofiler

Wrapper for clusterProfiler Tool
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**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.


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**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)

**Reference**

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)
author	proteore
date	Tue, 20 Mar 2018 08:59:51 -0400
parents	ad1244024bd8
children	4609346d8108