facopy

This package is for version 3.7 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see facopy.

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


Bioconductor version: 3.7

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.

Author: David Mosen-Ansorena

Maintainer: David Mosen-Ansorena <dmosen.gn at cicbiogune.es>

Citation (from within R, enter citation("facopy")):

Installation

To install this package, start R (version "3.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("facopy")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("facopy")
facopy PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews CopyNumberVariation, GeneSetEnrichment, Genetics, GenomicVariation, Microarray, Sequencing, Software, Visualization
Version 1.13.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License CC BY-NC 4.0
Depends R (>= 3.0), methods, cgdsr (>= 1.1.30), coin (>= 1.0), ggplot2, gridExtra, facopy.annot, grid
Imports annotate, data.table, DOSE, FactoMineR, GO.db, GOstats, graphite, igraph, S4Vectors, IRanges, MASS, nnet, reshape2, Rgraphviz, scales
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package facopy_1.13.0.tar.gz
Windows Binary facopy_1.13.0.zip
Mac OS X 10.11 (El Capitan) facopy_1.13.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/facopy
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/facopy
Package Short Url https://bioconductor.org/packages/facopy/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive