Mercurial > repos > proteore > proteore_goprofiles

annotate README.rst @ 4:715002a394ec draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit b36435833bf54f90f62cc240f2cda1c889161b23-dirty
author proteore
date Fri, 23 Mar 2018 10:47:17 -0400
parents ed226f0e5625
children 781072a65600
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
58a8ddd58dde planemo upload commit f338a1cf9a782938c228f9bd0ea19ef22eec35d8-dirty
proteore
parents: 0
diff changeset
1 Galaxy wrappers for goProfiles Tool
58a8ddd58dde planemo upload commit f338a1cf9a782938c228f9bd0ea19ef22eec35d8-dirty
proteore
parents: 0
diff changeset
2 ===================================
0
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
3
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
4 **Authors**
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
5
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
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.
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
7
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
8 **Galaxy integration**
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
9
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
10 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
11
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
12 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit,Migale Bioinformatics platform,
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
13
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
14 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
15
2
58a8ddd58dde planemo upload commit f338a1cf9a782938c228f9bd0ea19ef22eec35d8-dirty
proteore
parents: 0
diff changeset
16 -----------------------------------
0
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
17
3
ed226f0e5625 planemo upload commit 08f1831e097df5d74bf60ff5955e7e9c8e524cc8-dirty
proteore
parents: 2
diff changeset
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.
0
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
19
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
20 You can choose one or more GO categories:
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
21
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
22 * Biological Process (BP)
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
23 * Cellular Component (CC)
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
24 * Molecular Function (MF)
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
25
3
ed226f0e5625 planemo upload commit 08f1831e097df5d74bf60ff5955e7e9c8e524cc8-dirty
proteore
parents: 2
diff changeset
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.
0
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
27
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
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)
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
29
3
ed226f0e5625 planemo upload commit 08f1831e097df5d74bf60ff5955e7e9c8e524cc8-dirty
proteore
parents: 2
diff changeset
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.