To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("CODEX")

In most cases, you don't need to download the package archive at all.

CODEX

DOI: 10.18129/B9.bioc.CODEX    

This is the development version of CODEX; for the stable release version, see CODEX.

A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing

Bioconductor version: Development (3.6)

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("http://bioc.ism.ac.jp/biocLite.R")
biocLite("CODEX")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("CODEX")

 

PDF R Script Using CODEX
PDF   Reference Manual
Text   NEWS

Details

biocViews CopyNumberVariation, ExomeSeq, Normalization, QualityControl, Software
Version 1.9.0
In Bioconductor since BioC 3.1 (R-3.2) (2.5 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.

Source Package CODEX_1.9.0.tar.gz
Windows Binary CODEX_1.9.0.zip
Mac OS X 10.11 (El Capitan) CODEX_1.9.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CODEX
Package Short Url http://bioconductor.org/packages/CODEX/
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