Package: facopy
Type: Package
Title: Feature-based association and gene-set enrichment for copy
        number alteration analysis in cancer
Version: 1.3.1
Date: 2015-23-07
Author: David Mosen-Ansorena
Maintainer: David Mosen-Ansorena <dmosen.gn@cicbiogune.es>
Imports: annotate, data.table, DOSE, FactoMineR, GO.db, GOstats,
        graphite, igraph, IRanges, MASS, nnet, reshape2, Rgraphviz,
        scales
Depends: R (>= 3.0), methods, cgdsr (>= 1.1.30), coin (>= 1.0),
        ggplot2, gridExtra, facopy.annot, grid
Description: 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.
License: CC BY-NC 4.0
biocViews: Software, CopyNumberVariation, GeneSetEnrichment,
        GenomicVariation, Genetics, Microarray, Sequencing,
        Visualization
NeedsCompilation: no
Packaged: 2015-07-25 05:28:39 UTC; biocbuild
Built: R 3.2.1; ; 2015-07-25 08:33:25 UTC; windows
