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PureCN

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

Copy number calling and SNV classification using targeted short read sequencing


Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
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")
Best practices, quick start and command line usage HTML R Script
Overview of the PureCN R package PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews CopyNumberVariation, Coverage, ImmunoOncology, Sequencing, Software, VariantAnnotation, VariantDetection
Version 2.9.4
In Bioconductor since BioC 3.3 (R-3.3) (8 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, 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
See More
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

Package Archives

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

Source Package PureCN_2.9.4.tar.gz
Windows Binary PureCN_2.9.4.zip
macOS Binary (x86_64) PureCN_2.9.4.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/PureCN
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/PureCN
Bioc Package Browser https://code.bioconductor.org/browse/PureCN/
Package Short Url https://bioconductor.org/packages/PureCN/
Package Downloads Report Download Stats