DOI: 10.18129/B9.bioc.CODEX    

This package is for version 3.7 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: 3.7

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>

Citation (from within R, enter citation("CODEX")):


To install this package, start R and enter:

## try http:// if https:// URLs are not supported


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



PDF R Script Using CODEX
PDF   Reference Manual
Text   NEWS


biocViews CopyNumberVariation, ExomeSeq, Normalization, QualityControl, Software
Version 1.12.0
In Bioconductor since BioC 3.1 (R-3.2) (3.5 years)
License GPL-2
Depends R (>= 3.2.3), Rsamtools, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg19, IRanges, Biostrings, S4Vectors
Suggests WES.1KG.WUGSC
Depends On Me iCNV
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CODEX_1.12.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) CODEX_1.12.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: