- Home
- Bioconductor 3.0
- Software Packages
- HMMcopy
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("HMMcopy")
In most cases, you don't need to download the package archive at all.
HMMcopy
|
This package is for version 3.0 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: 3.0
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 <jujubix at cs.ubc.ca>, Gavin Ha <gha at bccrc.ca>, Sohrab Shah <sshah at bccrc.ca>
Citation (from within R,
enter citation("HMMcopy")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("HMMcopy")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("HMMcopy")
| R Script | HMMcopy | |
| Reference Manual |
Details
| biocViews | CopyNumberVariation, Microarray, Preprocessing, Sequencing, Software, Visualization |
| Version | 1.8.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (3.5 years) |
| License | GPL-3 |
| Depends | R (>= 2.10.0), IRanges(>= 1.4.16), geneplotter(>= 1.24.0) |
| Imports | |
| LinkingTo | |
| Suggests | |
| 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.
| Package Source | HMMcopy_1.8.0.tar.gz |
| Windows Binary | HMMcopy_1.8.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | HMMcopy_1.8.0.tgz |
| Mac OS X 10.9 (Mavericks) | HMMcopy_1.8.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/HMMcopy/tree/release-3.0 |
| Package Short Url | http://bioconductor.org/packages/HMMcopy/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
