To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("facopy")

In most cases, you don't need to download the package archive at all.

facopy

 

   

This is the development version of facopy; for the stable release version, see facopy.

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

Bioconductor version: Development (3.6)

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 and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/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 1.11.0
In Bioconductor since BioC 3.0 (R-3.1) (2.5 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
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source facopy_1.11.0.tar.gz
Windows Binary facopy_1.11.0.zip
Mac OS X 10.11 (El Capitan) facopy_1.11.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/facopy
Package Short Url http://bioconductor.org/packages/facopy/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: