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annotate README.rst @ 3:ed226f0e5625 draft

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author proteore
date Wed, 14 Mar 2018 12:51:53 -0400
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1 Galaxy wrappers for goProfiles Tool
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2 ===================================
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4 **Authors**
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6 Sanchez A, Ocana J and Salicru M (2016). goProfiles: goProfiles: an R package for the statistical analysis of functional profiles. R package version 1.38.0.
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8 **Galaxy integration**
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10 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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12 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit,Migale Bioinformatics platform,
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14 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
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16 -----------------------------------
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18 This tool, based on the goProfiles R package, performs statistical analysis of functional profiles. It is based on GO ontology and considers either a gene set ('Entrez’ Identifiers) or a protein set (Uniprot accession number) as input.
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20 You can choose one or more GO categories:
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22 * Biological Process (BP)
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23 * Cellular Component (CC)
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24 * Molecular Function (MF)
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26 Functional profile at a given GO level is obtained by counting the number of identifiers having a hit in each category of this level (2 by default). Results are displayed as bar plots (with absolute or relative frequencies) and can be exported in pdf, png and jpeg formats; textual output with GO terms and their computed frequencies is also provided.
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28 For more details about GoProfiles, please read: Salicrú et al. Comparison of lists of genes based on functional profiles. BMC Bioinformatics. 2011;12:401.(https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-401)
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30 If your type of identifiers is not supported (i.e. different from Uniprot and Entrez), please use the **ID Converter** tool in the ProteoRE section to convert your list of IDs first.