To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("PureCN")
In most cases, you don't need to download the package archive at all.
PureCN
|
This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see PureCN.
Copy number calling and SNV classification using targeted short read sequencing
Bioconductor version: 3.4
This package estimates tumor purity, copy number, loss of heterozygosity (LOH), and status of single nucleotide variants (SNVs). PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection pipelines, and has support for tumor samples without matching normal samples.
Author: Markus Riester
Maintainer: Markus Riester <markus.riester at novartis.com>
Citation (from within R,
enter citation("PureCN")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("PureCN")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("PureCN")
| R Script | PureCN | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | CopyNumberVariation, Coverage, Sequencing, Software, VariantAnnotation, VariantDetection |
| Version | 1.2.3 |
| In Bioconductor since | BioC 3.3 (R-3.3) (1 year) |
| License | Artistic-2.0 |
| Depends | R (>= 3.2), DNAcopy, VariantAnnotation(>= 1.14.1) |
| Imports | GenomicRanges(>= 1.20.3), IRanges(>= 2.2.1), RColorBrewer, S4Vectors, data.table, grDevices, graphics, stats, utils, SummarizedExperiment, GenomeInfoDb, Rsamtools, Biostrings |
| LinkingTo | |
| Suggests | PSCBS, RUnit, BiocStyle, BiocGenerics, knitr, getopt, rtracklayer |
| 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 | PureCN_1.2.3.tar.gz |
| Windows Binary | PureCN_1.2.3.zip |
| Mac OS X 10.9 (Mavericks) | PureCN_1.2.3.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/PureCN/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/PureCN/ |
| Package Downloads Report | Download Stats |
Documentation »
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