ACSNMineR

Package: ACSNMineR
Type: Package
Title: Gene Enrichment Analysis from ACSN Maps or GMT Files
Version: 0.16.01.29
Date: 2016-01-29
Authors@R: c(person("Paul", "Deveau", role = c("aut", "cre"),
email = "paul.deveau@curie.fr"),
person("Eric", "Bonnet",role = "aut",
email = "eric.bonnet@curie.fr"))
Maintainer: Paul Deveau <paul.deveau@curie.fr>
Description: Compute and represent gene set enrichment or depletion from your data based on pre-saved maps from the Atlas of Cancer Signalling Networks (ACSN) or user imported maps.
User imported maps must be complying with the GMT format as defined by the Broad Institute, that is to say that the file should be tab-separated, that the first column should contain the module name, the second column can contain comments that will be overwritten with the number of genes in the module, and subsequent columns must contain the list of genes (HUGO symbols; tab-separated) inside the module.
The gene set enrichment can be run with hypergeometric test or Fisher exact test, and can use multiple corrections.
Visualization of data can be done either by barplots or heatmaps.
Depends: R (>= 3.1.0), ggplot2, gridExtra, scales,
Suggests: knitr, rmarkdown,
License: GPL-2
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-02-12 10:01:07 UTC; User
Author: Paul Deveau [aut, cre],
Eric Bonnet [aut]
Repository: CRAN
Date/Publication: 2016-02-12 11:08:48

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'ACSNMineR' ...
** package 'ACSNMineR' successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'ACSNMineR'
    finding HTML links ... done
    ACSN_maps                               html  
    cnum                                    html  
    enrichment                              html  
    enrichment_test                         html  
    format_from_gmt                         html  
    genes_test                              html  
    multisample_enrichment                  html  
    p.val.calc                              html  
    represent_enrichment                    html  
    reverselog_trans                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ACSNMineR)
Making 'packages.html' ... done