PureCN
Copy number calling and SNV classification using targeted short read sequencing
Bioconductor version: Release (3.20)
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("PureCN")):
Installation
To install this package, start R (version "4.4") 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")| Best practices, quick start and command line usage | HTML | R Script |
| Overview of the PureCN R package | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CopyNumberVariation, Coverage, ImmunoOncology, Sequencing, Software, VariantAnnotation, VariantDetection |
| Version | 2.12.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8.5 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 |
| 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_2.12.0.tar.gz |
| Windows Binary (x86_64) | PureCN_2.12.0.zip |
| macOS Binary (x86_64) | PureCN_2.12.0.tgz |
| macOS Binary (arm64) | PureCN_2.11.0.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/ |
| Package Downloads Report | Download Stats |