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

DOI: 10.18129/B9.bioc.PureCN

Copy number calling and SNV classification using targeted short read sequencing

Bioconductor version: Release (3.5)

This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number pipelines, and has support for tumor samples without matching normal samples.

Author: Markus Riester [aut, cre], Angad P. Singh [aut]

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 overview
PDF R Script Quick start and command line usage
PDF Reference Manual
Text NEWS

Details

biocViews CopyNumberVariation, Coverage, Sequencing, Software, VariantAnnotation, VariantDetection
Version 1.6.3
In Bioconductor since BioC 3.3 (R-3.3) (1.5 years)
License Artistic-2.0
Depends R (>= 3.3), 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, rtracklayer, ggplot2, futile.logger, VGAM, edgeR, limma
LinkingTo
Suggests PSCBS, RUnit, BiocStyle, BiocGenerics, knitr, getopt, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
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.

Source Package PureCN_1.6.3.tar.gz
Windows Binary PureCN_1.6.3.zip
Mac OS X 10.11 (El Capitan) PureCN_1.6.3.tgz
Source Repository git clone https://git.bioconductor.org/packages/PureCN
Package Short Url http://bioconductor.org/packages/PureCN/
Package Downloads Report Download Stats

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