Mercurial > repos > proteore > proteore_clusterprofiler
changeset 34:f078633d9669 draft
planemo upload commit a172073d58a2fc713af8656d3bcfa28592dcc242-dirty
| author | proteore |
|---|---|
| date | Mon, 03 Jun 2019 09:46:18 -0400 |
| parents | 4b29214f2d4c |
| children | 6a0d0b5b91f2 |
| files | GO-enrich.R README.rst cluster_profiler.xml |
| diffstat | 3 files changed, 18 insertions(+), 2 deletions(-) [+] |
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--- a/GO-enrich.R Tue May 14 09:36:23 2019 -0400 +++ b/GO-enrich.R Mon Jun 03 09:46:18 2019 -0400 @@ -1,5 +1,5 @@ options(warn=-1) #TURN OFF WARNINGS !!!!!! -suppressMessages(library(clusterProfiler,quietly = TRUE)) +#suppressMessages(library(clusterProfiler,quietly = TRUE)) # Read file and return file content as data.frame read_file <- function(path,header){
--- a/README.rst Tue May 14 09:36:23 2019 -0400 +++ b/README.rst Mon Jun 03 09:46:18 2019 -0400 @@ -40,6 +40,13 @@ Text (tables) and graphics representing the repartition and/or enrichment of GO categories. +**Packages used** + - bioconductor-org.hs.eg.db v3.5.0 + - bioconductor-org.mm.eg.db v3.5.0 + - bioconductor-org.rn.eg.db v3.5.0 + - dose v3.2.0 + - clusterpofiler v 3.4.4 + **User manual / Documentation** of the clusterProfiler R package (functions and parameters): https://bioconductor.org/packages/3.7/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html (Very well explained) \ No newline at end of file
--- a/cluster_profiler.xml Tue May 14 09:36:23 2019 -0400 +++ b/cluster_profiler.xml Mon Jun 03 09:46:18 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="cluter_profiler" name="GO terms classification and enrichment analysis" version="2019.05.14"> +<tool id="cluter_profiler" name="GO terms classification and enrichment analysis" version="2019.06.01"> <description>(Human, Mouse, Rat)[clusterProfiler]</description> <requirements> <requirement type="package" version="3.4.1">R</requirement> @@ -282,6 +282,15 @@ .. class:: infomark +Packages used: + - bioconductor-org.hs.eg.db v3.5.0 + - bioconductor-org.mm.eg.db v3.5.0 + - bioconductor-org.rn.eg.db v3.5.0 + - dose v3.2.0 + - clusterpofiler v 3.4.4 + +.. class:: infomark + **Galaxy integration** T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR