To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("PureCN")
In most cases, you don't need to download the package archive at all.
PureCN
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Copy number calling and SNV classification using targeted short read sequencing
Bioconductor version: Release (3.5)
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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("PureCN")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("PureCN")
| R Script | PureCN overview | |
| R Script | Quick start and command line usage | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | CopyNumberVariation, Coverage, Sequencing, Software, VariantAnnotation, VariantDetection |
| Version | 1.6.3 |
| In Bioconductor since | BioC 3.3 (R-3.3) (1.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.3), DNAcopy, VariantAnnotation(>= 1.14.1) |
| Imports | GenomicRanges(>= 1.20.3), IRanges(>= 2.2.1), RColorBrewer, S4Vectors, data.table, grDevices, graphics, stats, utils, SummarizedExperiment, GenomeInfoDb, Rsamtools, Biostrings, rtracklayer, ggplot2, futile.logger, VGAM, edgeR, limma |
| LinkingTo | |
| Suggests | PSCBS, RUnit, BiocStyle, BiocGenerics, knitr, getopt, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | PureCN_1.6.3.tar.gz |
| Windows Binary | PureCN_1.6.3.zip |
| Mac OS X 10.11 (El Capitan) | PureCN_1.6.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/PureCN |
| Package Short Url | http://bioconductor.org/packages/PureCN/ |
| Package Downloads Report | Download Stats |
Documentation »
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