PureCN

DOI: 10.18129/B9.bioc.PureCN    

This package is for version 3.9 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: 3.9

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 (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("PureCN")

For older versions of R, please refer to the appropriate Bioconductor release.

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, ImmunoOncology, Sequencing, Software, VariantAnnotation, VariantDetection
Version	1.14.3
In Bioconductor since	BioC 3.3 (R-3.3) (3.5 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, GenomicFeatures, Rsamtools, Biostrings, BiocGenerics, rtracklayer, ggplot2, gridExtra, futile.logger, VGAM, tools, methods, rhdf5, Matrix
LinkingTo
Suggests	PSCBS, copynumber, BiocStyle, BiocParallel, knitr, optparse, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, covr, testthat
SystemRequirements
Enhances
URL	https://github.com/lima1/PureCN
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	PureCN_1.14.3.tar.gz
Windows Binary	PureCN_1.14.3.zip
Mac OS X 10.11 (El Capitan)	PureCN_1.14.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/PureCN
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/PureCN
Package Short Url	https://bioconductor.org/packages/PureCN/
Package Downloads Report	Download Stats