ACSNMineR: Gene Enrichment Analysis from ACSN Maps or GMT Files

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.

Install the latest version of this package by entering the following in R:
install.packages("ACSNMineR")
AuthorPaul Deveau [aut, cre], Eric Bonnet [aut]
Date of publication2016-09-01 17:30:55
MaintainerPaul Deveau <paul.deveau@curie.fr>
LicenseGPL-2
Version0.16.8.25

View on CRAN

Files

inst
inst/extdata
inst/extdata/cellcycle_short.gmt
inst/doc
inst/doc/ACSN_map_updating.Rmd
inst/doc/ACSN-vignette.Rmd
inst/doc/ACSN_map_updating.html
inst/doc/ACSN_map_updating.R inst/doc/ACSN-vignette.R
inst/doc/ACSN-vignette.html
NAMESPACE
data
data/ACSN_maps.rda
data/genes_test.rda
data/enrichment_test.rda
R
R/plots.R R/data_handling.R R/ACSN_Enrichment.R
vignettes
vignettes/ACSN_map_updating.Rmd
vignettes/ACSN-vignette.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/format_from_gmt.Rd man/reverselog_trans.Rd man/p.val.calc.Rd man/enrichment.Rd man/Create_master_map.Rd man/ACSN_maps.Rd man/genes_test.Rd man/cnum.Rd man/represent_enrichment.Rd man/enrichment_test.Rd man/multisample_enrichment.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.