PureCN

DOI: 10.18129/B9.bioc.PureCN    

Copy number calling and SNV classification using targeted short read sequencing

Bioconductor version: Release (3.11)

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 (version "4.0") 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")

 

HTML R Script Best practices, quick start and command line usage
PDF R Script Overview of the PureCN R package
PDF   Reference Manual
Text   NEWS

Details

biocViews CopyNumberVariation, Coverage, ImmunoOncology, Sequencing, Software, VariantAnnotation, VariantDetection
Version 1.18.1
In Bioconductor since BioC 3.3 (R-3.3) (4.5 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 BiocParallel, BiocStyle, PSCBS, TxDb.Hsapiens.UCSC.hg19.knownGene, copynumber, covr, knitr, optparse, org.Hs.eg.db, rmarkdown, 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_1.18.1.tar.gz
Windows Binary PureCN_1.18.1.zip
macOS 10.13 (High Sierra) PureCN_1.18.1.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
Old Source Packages for BioC 3.11 Source Archive

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