DOI: 10.18129/B9.bioc.PureCN  

Copy number calling and SNV classification using targeted short read sequencing

Bioconductor version: Release (3.17)

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>

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biocViews CopyNumberVariation, Coverage, ImmunoOncology, Sequencing, Software, VariantAnnotation, VariantDetection
Version 2.6.4
In Bioconductor since BioC 3.3 (R-3.3) (7.5 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, GenomeInfoDb, GenomicFeatures, Rsamtools, Biobase, Biostrings, BiocGenerics, rtracklayer, ggplot2, gridExtra, futile.logger, VGAM, tools, methods, mclust, rhdf5, Matrix
Suggests BiocParallel, BiocStyle, PSCBS, R.utils, TxDb.Hsapiens.UCSC.hg19.knownGene, covr, knitr, optparse, org.Hs.eg.db, jsonlite, markdown, rmarkdown, testthat
Enhances genomicsdb (>= 0.0.3), copynumber
URL https://github.com/lima1/PureCN
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Source Package PureCN_2.6.4.tar.gz
Windows Binary PureCN_2.6.4.zip
macOS Binary (x86_64)
macOS Binary (arm64) PureCN_2.6.4.tgz
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/
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