ACSNMineR: Gene Enrichment Analysis from ACSN Maps or GMT Files

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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.

Author
Paul Deveau [aut, cre], Eric Bonnet [aut]
Date of publication
2016-09-01 17:30:55
Maintainer
Paul Deveau <paul.deveau@curie.fr>
License
GPL-2
Version
0.16.8.25

View on CRAN

Man pages

ACSN_maps
Atlas of Cancer Signalling Networks
cnum
Convert to numeric
Create_master_map
From a list of maps, create or replace a master
enrichment
Gene set enrichment analysis
enrichment_test
Result from enrichment test of "genes_test" on the ACSN maps
format_from_gmt
Import data from gmt files Convert gmt file to dataframe that...
genes_test
Set of genes to test map
multisample_enrichment
Automated gene set analysis for multiple sets
p.val.calc
Calculate p-value
represent_enrichment
Graphic representation of enrichment
reverselog_trans
Scale for barplots and heatmaps

Files in this package

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