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

 

   

Copy number calling and SNV classification using targeted short read sequencing

Bioconductor version: Release (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")

 

PDF R Script PureCN
PDF   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

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