facopy

DOI: 10.18129/B9.bioc.facopy    

This package is for version 3.7 of Bioconductor; for the 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>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("facopy")

Documentation

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

browseVignettes("facopy")

 

PDF	R Script	facopy
PDF		Reference Manual
Text		NEWS

Details

biocViews	CopyNumberVariation, GeneSetEnrichment, Genetics, GenomicVariation, Microarray, Sequencing, Software, Visualization
Version	1.13.0
In Bioconductor since	BioC 3.0 (R-3.1) (4 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
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

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	http://bioconductor.org/packages/facopy/
Package Downloads Report	Download Stats