HMMcopy

DOI: 10.18129/B9.bioc.HMMcopy  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see HMMcopy.

Copy number prediction with correction for GC and mappability bias for HTS data

Bioconductor version: 3.16

Corrects GC and mappability biases for readcounts (i.e. coverage) in non-overlapping windows of fixed length for single whole genome samples, yielding a rough estimate of copy number for furthur analysis. Designed for rapid correction of high coverage whole genome tumour and normal samples.

Author: Daniel Lai, Gavin Ha, Sohrab Shah

Maintainer: Daniel Lai <dalai at bccrc.ca>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("HMMcopy")

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("HMMcopy")

 

PDF	R Script	HMMcopy
PDF		Reference Manual

Details

biocViews	CopyNumberVariation, Microarray, Preprocessing, Sequencing, Software, Visualization
Version	1.40.0
In Bioconductor since	BioC 2.11 (R-2.15) (10.5 years)
License	GPL-3
Depends	R (>= 2.10.0), data.table (>= 1.11.8)
Imports
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	qsea
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	HMMcopy_1.40.0.tar.gz
Windows Binary	HMMcopy_1.40.0.zip
macOS Binary (x86_64)	HMMcopy_1.40.0.tgz
macOS Binary (arm64)	HMMcopy_1.40.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/HMMcopy
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/HMMcopy
Bioc Package Browser	https://code.bioconductor.org/browse/HMMcopy/
Package Short Url	https://bioconductor.org/packages/HMMcopy/
Package Downloads Report	Download Stats