To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("facopy")
In most cases, you don't need to download the package archive at all.
facopy
|
This package is for version 3.4 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: 3.4
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("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")
| R Script | facopy | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | CopyNumberVariation, GeneSetEnrichment, Genetics, GenomicVariation, Microarray, Sequencing, Software, Visualization |
| Version | 1.8.0 |
| 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_1.8.0.tar.gz |
| Windows Binary | facopy_1.8.0.zip |
| Mac OS X 10.9 (Mavericks) | facopy_1.8.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/facopy/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/facopy/ |
| Package Downloads Report | Download Stats |
Documentation »
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