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1 Wrapper for clusterProfiler Tool
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2 ================================
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4 **Authors**
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6 clusterProfiler R package reference :
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7 G Yu, LG Wang, Y Han, QY He. clusterProfiler: an R package for comparing biological themes among gene clusters.
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8 OMICS: A Journal of Integrative Biology 2012, 16(5):284-287.
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9 doi:[10.1089/omi.2011.0118](http://dx.doi.org/10.1089/omi.2011.0118)
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12 **Galaxy integration**
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14 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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16 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
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18 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
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20 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
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23 --------------------------------
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25 **Galaxy component based on R package clusterProfiler (see ref below)**
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27 This component allows to perform GO enrichment-analyses.
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28 Given a list of IDs, the tool either
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29 (i) performs gene classification based on GO distribution at a specific level, or
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30 (ii) calculates GO categories enrichment (over- or under-representation) for the IDs of the input list,
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31 compared to a background (whole organism or user-defined list).
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33 **Input required**
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34
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35 This component works with Gene ids (e.g : 4151, 7412) or Uniprot accession number (e.g. P31946).
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36 You can copy/paste these identifiers or supply a tabular file (.csv, .tsv, .txt, .tab) where there are contained.
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38
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39 **Output**
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40
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41 Text (tables) and graphics representing the repartition and/or enrichment of GO categories.
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43 **Packages used**
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44 - bioconductor-org.hs.eg.db v3.5.0
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45 - bioconductor-org.mm.eg.db v3.5.0
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46 - bioconductor-org.rn.eg.db v3.5.0
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47 - dose v3.2.0
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48 - clusterpofiler v 3.4.4
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49
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50 **User manual / Documentation** of the clusterProfiler R package (functions and parameters):
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51 https://bioconductor.org/packages/3.7/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html
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52 (Very well explained)