PureCN

DOI: 10.18129/B9.bioc.PureCN    

Copy number calling and SNV classification using targeted short read sequencing

Bioconductor version: Release (3.6)

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>

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	1.8.1
In Bioconductor since	BioC 3.3 (R-3.3) (2 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, GenomicFeatures, Rsamtools, Biostrings, BiocGenerics, rtracklayer, ggplot2, futile.logger, VGAM, edgeR, tools, limma
LinkingTo
Suggests	PSCBS, RUnit, BiocStyle, knitr, optparse, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
SystemRequirements
Enhances
URL	https://github.com/lima1/PureCN
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_1.8.1.tar.gz
Windows Binary	PureCN_1.8.1.zip
Mac OS X 10.11 (El Capitan)	PureCN_1.8.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/PureCN
Package Short Url	http://bioconductor.org/packages/PureCN/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive