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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("HMMcopy")
In most cases, you don't need to download the package archive at all.
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:
source("http://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) |
| 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 |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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