Mercurial > repos > proteore > proteore_clusterprofiler

comparison README.rst @ 3:ad1244024bd8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 08f1831e097df5d74bf60ff5955e7e9c8e524cc8-dirty
author proteore
date Wed, 14 Mar 2018 12:40:35 -0400
parents a71792aa5a08
children 4609346d8108
comparison
equal deleted inserted replaced
2:a71792aa5a08 3:ad1244024bd8
29 (i) performs gene classification based on GO distribution at a specific level, or 29 (i) performs gene classification based on GO distribution at a specific level, or
30 (ii) calculates GO categories enrichment (over- or under-representation) for the IDs of the input list, 30 (ii) calculates GO categories enrichment (over- or under-representation) for the IDs of the input list,
31 compared to a background (whole organism or user-defined list). 31 compared to a background (whole organism or user-defined list).
32 32
33 **Input required** 33 **Input required**
34 34
35 This component works with Gene ids (e.g : 4151, 7412) or Uniprot accession number (e.g. P31946). 35 This component works with Gene ids (e.g : 4151, 7412) or Uniprot accession number (e.g. P31946).
36 You can copy/paste these identifiers or supply a tabular file (.csv, .tsv, .txt, .tab) where there are contained. 36 You can copy/paste these identifiers or supply a tabular file (.csv, .tsv, .txt, .tab) where there are contained.
37 37
38 38
39 **Output** 39 **Output**
41 Text (tables) and graphics representing the repartition and/or enrichment of GO categories. 41 Text (tables) and graphics representing the repartition and/or enrichment of GO categories.
42 42
43 **User manual / Documentation** of the clusterProfiler R package (functions and parameters): 43 **User manual / Documentation** of the clusterProfiler R package (functions and parameters):
44 https://bioconductor.org/packages/3.7/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html 44 https://bioconductor.org/packages/3.7/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html
45 (Very well explained) 45 (Very well explained)
46
47 **Reference**
48
49 clusterProfiler R package reference :
50 G Yu, LG Wang, Y Han, QY He. clusterProfiler: an R package for comparing biological themes among gene clusters.
51 OMICS: A Journal of Integrative Biology 2012, 16(5):284-287.
52 doi:[10.1089/omi.2011.0118](http://dx.doi.org/10.1089/omi.2011.0118)