## try http:// if https:// URLs are not supported source("//www.anjoumacpherson.com/biocLite.R") biocLite("facopy")

This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, seefacopy.

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

Bioconductor version: 3.2

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported source("//www.anjoumacpherson.com/biocLite.R") biocLite("facopy")

Documentation

查看文档的版本包age installed in your system, start R and enter:

browseVignettes("facopy")

PDF		facopy
PDF		Reference Manual
Text		NEWS

Details

biocViews	CopyNumberVariation,GeneSetEnrichment,Genetics,GenomicVariation,Microarray,Sequencing,Software,Visualization
Version	1.4.1
In Bioconductor since	BioC 3.0 (R-3.1) (1.5 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,IRanges,MASS,nnet,reshape2,Rgraphviz,scales
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Build Report

Package Archives

Followbob 体育网址 instructions to use this package in your R session.

Package Source	facopy_1.4.1.tar.gz
Windows Binary	facopy_1.4.1.zip
Mac OS X 10.6 (Snow Leopard)	facopy_1.4.0.tgz
Mac OS X 10.9 (Mavericks)	facopy_1.4.1.tgz
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/facopy/tree/release-3.2
Package Short Url	//www.anjoumacpherson.com/packages/facopy/
Package Downloads Report	Download Stats