HMMcopy
Copy number prediction with correction for GC and mappability bias for HTS data
Bioconductor version: Release (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("HMMcopy")
):
Installation
To install this package, start R (version "4.4") 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")
HMMcopy | R Script | |
Reference Manual |
Details
biocViews | CopyNumberVariation, Microarray, Preprocessing, Sequencing, Software, Visualization |
Version | 1.46.0 |
In Bioconductor since | BioC 2.11 (R-2.15) (12 years) |
License | GPL-3 |
Depends | R (>= 2.10.0), data.table (>= 1.11.8) |
Imports | |
System Requirements | |
URL |
See More
Suggests | |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | qsea |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | HMMcopy_1.46.0.tar.gz |
Windows Binary | HMMcopy_1.46.0.zip |
macOS Binary (x86_64) | HMMcopy_1.46.0.tgz |
macOS Binary (arm64) | HMMcopy_1.46.0.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 |