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.

AuthorDavid Mosen-Ansorena
Date of publicationNone
MaintainerDavid Mosen-Ansorena <dmosen.gn@cicbiogune.es>
LicenseCC BY-NC 4.0
Version1.8.0

View on Bioconductor

Files in this package

facopy/DESCRIPTION
facopy/NAMESPACE
facopy/R
facopy/R/AllClasses.R facopy/R/AllGenerics.R
facopy/R/facopy_internal_v45.r
facopy/R/show-methods.R facopy/R/summary-methods.R
facopy/build
facopy/build/vignette.rds
facopy/data
facopy/data/myCalls.rda
facopy/data/myStudy.rda
facopy/data/myVariables.rda
facopy/inst
facopy/inst/CITATION
facopy/inst/NEWS
facopy/inst/doc
facopy/inst/doc/facopy.R
facopy/inst/doc/facopy.Rnw
facopy/inst/doc/facopy.pdf
facopy/man
facopy/man/addFeatures.Rd facopy/man/addVariables.Rd facopy/man/alterationSummary.Rd facopy/man/calculateCor.Rd facopy/man/facopy-package.Rd facopy/man/facopy.Rd facopy/man/facopyEnrichment.Rd facopy/man/facopyInfo-class.Rd facopy/man/facopyPlot.Rd facopy/man/getFacopyInfo.Rd facopy/man/myCalls.Rd facopy/man/myStudy.Rd facopy/man/myVariables.Rd facopy/man/plotBar.Rd facopy/man/plotHist.Rd facopy/man/plotPCA.Rd facopy/man/plotZoom.Rd facopy/man/preview.Rd facopy/man/readCNData.Rd facopy/man/variableCor.Rd facopy/man/variableSummary.Rd
facopy/vignettes
facopy/vignettes/enrichmentGO.pdf
facopy/vignettes/enrichmentPathway.pdf
facopy/vignettes/facopy.Rnw
facopy/vignettes/facopy.bib

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.