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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("exomeCopy")
In most cases, you don't need to download the package archive at all.
exomeCopy
Copy number variant detection from exome sequencing read depth
Bioconductor version: 3.0
Detection of copy number variants (CNV) from exome sequencing samples, including unpaired samples. The package implements a hidden Markov model which uses positional covariates, such as background read depth and GC-content, to simultaneously normalize and segment the samples into regions of constant copy count.
Author: Michael Love
Maintainer: Michael Love <michaelisaiahlove at gmail.com>
Citation (from within R,
enter citation("exomeCopy")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("exomeCopy")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("exomeCopy")
| R Script | Copy number variant detection in exome sequencing data | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | CopyNumberVariation, Genetics, Sequencing, Software |
| Version | 1.12.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) |
| License | GPL (>= 2) |
| Depends | IRanges, GenomicRanges, Rsamtools |
| Imports | stats4, methods, GenomeInfoDb |
| LinkingTo | |
| Suggests | Biostrings |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | Rariant, SomaticCancerAlterations |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | exomeCopy_1.12.0.tar.gz |
| Windows Binary | exomeCopy_1.12.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | exomeCopy_1.12.0.tgz |
| Mac OS X 10.9 (Mavericks) | exomeCopy_1.12.0.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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