facopy: Feature-based association and gene-set enrichment for copy number alteration analysis in cancer

facopy is an R package for fine-tuned cancer CNA association modeling. Association is measured directly at the genomic features of interest and, in the case of genes, downstream gene-set enrichment analysis can be performed thanks to novel internal processing of the data. The software opens a way to systematically scrutinize the differences in CNA distribution across tumoral phenotypes, such as those that relate to tumor type, location and progression. Currently, the output format from 11 different methods that analyze data from whole-genome/exome sequencing and SNP microarrays, is supported. Multiple genomes, alteration types and variable types are also supported.

Package details

AuthorDavid Mosen-Ansorena
Bioconductor views CopyNumberVariation GeneSetEnrichment Genetics GenomicVariation Microarray Sequencing Software Visualization
MaintainerDavid Mosen-Ansorena <dmosen.gn@cicbiogune.es>
LicenseCC BY-NC 4.0
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
if (!requireNamespace("BiocManager", quietly = TRUE))


Try the facopy package in your browser

Any scripts or data that you put into this service are public.

facopy documentation built on May 2, 2018, 2:30 a.m.