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Bioconductor - PureCN

PureCN

This is the released version of PureCN; for the devel version, see PureCN.

Copy number calling and SNV classification using targeted short read sequencing

Bioconductor version: Release (3.21)

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 novartis.com>

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

To install this package, start R (version "4.5") and enter:


if (!require("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")
Details biocViews CopyNumberVariation, Coverage, ImmunoOncology, Sequencing, Software, VariantAnnotation, VariantDetection Version 2.14.1 In Bioconductor since BioC 3.3 (R-3.3) (9 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.

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