To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("facopy")
In most cases, you don't need to download the package archive at all.
facopy
Feature-based association and gene-set enrichment for copy number alteration analysis in cancer
Bioconductor version: 3.0
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:
source("http://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 | 1.0.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) |
| License | CC BY-NC 4.0 |
| Depends | R (>= 3.0), methods, cgdsr (>= 1.1.30), coin (>= 1.0), ggplot2, gridExtra, facopy.annot |
| Imports | annotate, data.table, DOSE, FactoMineR, GO.db, GOstats, graphite, igraph, 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_1.0.0.tar.gz |
| Windows Binary | facopy_1.0.0.zip |
| Mac OS X 10.6 (Snow Leopard) | facopy_1.0.0.tgz |
| Mac OS X 10.9 (Mavericks) | facopy_1.0.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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