Mercurial > repos > proteore > proteore_pathview_mapping

annotate README.rst @ 8:33c9bd75882a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 1953798eb28b6e45c78342ed4c6a6a978d096fca
author proteore
date Thu, 30 Aug 2018 06:12:51 -0400
parents 097bb3ed2b4d
children 9fe4a861601b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
097bb3ed2b4d planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
1 Wrapper for Pathview tool
097bb3ed2b4d planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
2 =============================
097bb3ed2b4d planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
3
097bb3ed2b4d planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
4 **Authors**
097bb3ed2b4d planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
5
097bb3ed2b4d planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
6 David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
097bb3ed2b4d planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
7
097bb3ed2b4d planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
8 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
097bb3ed2b4d planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
9
097bb3ed2b4d planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
10 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
097bb3ed2b4d planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
11
097bb3ed2b4d planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
12 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
097bb3ed2b4d planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
13
097bb3ed2b4d planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
14 =============================
097bb3ed2b4d planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
15
097bb3ed2b4d planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
16 This tool map a list of Uniprot Accession number or Entrez gene ID to KEGG pathway with pathview R package.
097bb3ed2b4d planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
17
8
33c9bd75882a planemo upload commit 1953798eb28b6e45c78342ed4c6a6a978d096fca
proteore
parents: 0
diff changeset
18 Select your identifier type : UniprotAC or Entrez gene ID
33c9bd75882a planemo upload commit 1953798eb28b6e45c78342ed4c6a6a978d096fca
proteore
parents: 0
diff changeset
19
0
097bb3ed2b4d planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
20 Select an input file containing ids in a column, set header and column number or copy/paste your ids.
097bb3ed2b4d planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
21
8
33c9bd75882a planemo upload commit 1953798eb28b6e45c78342ed4c6a6a978d096fca
proteore
parents: 0
diff changeset
22 You can import 1 to 3 column(s) of expression values if you are importing ids from a file.
33c9bd75882a planemo upload commit 1953798eb28b6e45c78342ed4c6a6a978d096fca
proteore
parents: 0
diff changeset
23
33c9bd75882a planemo upload commit 1953798eb28b6e45c78342ed4c6a6a978d096fca
proteore
parents: 0
diff changeset
24 Select a species of interest.
0
097bb3ed2b4d planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
25
8
33c9bd75882a planemo upload commit 1953798eb28b6e45c78342ed4c6a6a978d096fca
proteore
parents: 0
diff changeset
26 Select one or several pathways of interest from the dropdown menu or copy/paste KEGG pathway id(s) or import it from a file.
0
097bb3ed2b4d planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
27
8
33c9bd75882a planemo upload commit 1953798eb28b6e45c78342ed4c6a6a978d096fca
proteore
parents: 0
diff changeset
28 Select the graph format : KEGG (jpg) or graphviz (pdf)
0
097bb3ed2b4d planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
29
097bb3ed2b4d planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
30 Uniprot accession number converted to Entrez geneID or Entrez geneID are mapped to each selected pathways.
097bb3ed2b4d planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
31
097bb3ed2b4d planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
32 Output : One file (png or pdf) for each selected pathway.