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HMMcopy

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

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

DOI: 10.18129/B9.bioc.HMMcopy

Bioconductor version: Development (3.24)

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: Andrew McPherson <andrew.mcpherson at gmail.com>

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

Daniel Lai, Gavin Ha, Sohrab Shah. HMMcopy: Copy number prediction with correction for GC and mappability bias for HTS data. doi:10.18129/B9.bioc.HMMcopy, R package version 1.55.1, https://bioconductor.org/packages/HMMcopy.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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")

Details

Package Archives

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