PureCN

This is the development version of PureCN; for the stable release version, see PureCN.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3

Copy number calling and SNV classification using targeted short read sequencing

Bioconductor version: Development (3.24)

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] ORCID: 0000-0002-4759-8332 , Angad P. Singh [aut]

Maintainer: Markus Riester <markus.riester at gmail.com>

Citation (from within R, enter citation("PureCN")):

Markus Riester, Angad P. Singh. PureCN: Copy number calling and SNV classification using targeted short read sequencing. doi:10.18129/B9.bioc.PureCN, R package version 2.19.0, https://bioconductor.org/packages/PureCN.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CopyNumberVariation, Coverage, ImmunoOncology, Sequencing, Software, VariantAnnotation, VariantDetection
Version	2.19.0
In Bioconductor since	BioC 3.3 (R-3.3) (10.5 years)
License	Artistic-2.0
Depends	R (>= 3.5.0), DNAcopy, VariantAnnotation (>= 1.14.1)
Imports	GenomicRanges (>= 1.20.3), IRanges (>= 2.2.1), RColorBrewer, S4Vectors, data.table, grDevices, graphics, stats, utils, SummarizedExperiment, Seqinfo, GenomeInfoDb, GenomicFeatures, Rsamtools, Biobase, Biostrings, BiocGenerics, rtracklayer, ggplot2, gridExtra, futile.logger, VGAM, tools, methods, mclust, rhdf5, Matrix
System Requirements
URL	https://github.com/lima1/PureCN
Bug Reports	https://github.com/lima1/PureCN/issues

Suggests	BiocParallel, BiocStyle, PSCBS, R.utils, TxDb.Hsapiens.UCSC.hg19.knownGene, covr, knitr, optparse, org.Hs.eg.db, jsonlite, markdown, rmarkdown, testthat
Linking To
Enhances	genomicsdb (>= 0.0.3)
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	PureCN_2.19.0.tar.gz
Windows Binary (x86_64)	PureCN_2.19.0.zip
macOS Binary (big-sur-x86_64)	PureCN_2.19.0.tgz
macOS Binary (sonoma-arm64)	PureCN_2.19.0.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