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HMMcopy

This is the development version of HMMcopy; for the stable release version, see HMMcopy.

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


Bioconductor version: Development (3.19)

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>

Citation (from within R, enter citation("HMMcopy")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
HMMcopy PDF R Script
Reference Manual PDF

Details

biocViews CopyNumberVariation, Microarray, Preprocessing, Sequencing, Software, Visualization
Version 1.45.0
In Bioconductor since BioC 2.11 (R-2.15) (11.5 years)
License GPL-3
Depends R (>= 2.10.0), data.table (>= 1.11.8)
Imports
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Package Archives

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

Source Package HMMcopy_1.45.0.tar.gz
Windows Binary HMMcopy_1.45.0.zip
macOS Binary (x86_64) HMMcopy_1.45.0.tgz
macOS Binary (arm64) HMMcopy_1.45.0.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