To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CODEX")
In most cases, you don't need to download the package archive at all.
CODEX
|
This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see CODEX.
A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing
Bioconductor version: 3.4
A normalization and copy number variation calling procedure for whole exome DNA sequencing data. CODEX relies on the availability of multiple samples processed using the same sequencing pipeline for normalization, and does not require matched controls. The normalization model in CODEX includes terms that specifically remove biases due to GC content, exon length and targeting and amplification efficiency, and latent systemic artifacts. CODEX also includes a Poisson likelihood-based recursive segmentation procedure that explicitly models the count-based exome sequencing data.
Author: Yuchao Jiang, Nancy R. Zhang
Maintainer: Yuchao Jiang <yuchaoj at wharton.upenn.edu>
Citation (from within R,
enter citation("CODEX")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CODEX")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CODEX")
| R Script | Using CODEX | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | CopyNumberVariation, ExomeSeq, Normalization, QualityControl, Software |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (2 years) |
| License | GPL-2 |
| Depends | R (>= 3.2.3), Rsamtools, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg19, IRanges, Biostrings, S4Vectors |
| Imports | |
| LinkingTo | |
| Suggests | WES.1KG.WUGSC |
| 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 | CODEX_1.6.0.tar.gz |
| Windows Binary | CODEX_1.6.0.zip |
| Mac OS X 10.9 (Mavericks) | CODEX_1.6.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/CODEX/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/CODEX/ |
| 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
