PureCN
Copy number calling and SNV classification using targeted short read sequencing
Bioconductor version: 3.24 · Package version: 2.19.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("PureCN")Details
| Maintainer | Markus Riester <markus.riester@gmail.com> |
| Author | Markus Riester [aut, cre] (ORCID: <https://orcid.org/0000-0002-4759-8332>), Angad P. Singh [aut] |
| License | Artistic-2.0 |
| URL | https://github.com/lima1/PureCN |
| Bug Reports | https://github.com/lima1/PureCN/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | CopyNumberVariation, Coverage, ImmunoOncology, Sequencing, Software, VariantAnnotation, VariantDetection |
| Package Short Url | https://bioconductor.org/packages/PureCN/ |
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.
Documentation
Download
Follow the 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 (arm64) | PureCN_2.19.0.tgz |
| macOS binary (x86_64) | PureCN_2.19.0.tgz |
Dependencies
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
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)