Registration Open for Bioc2024 July 24-26


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 (3.20)

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 (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


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

Using CODEX PDF R Script
Reference Manual PDF


biocViews CopyNumberVariation, ExomeSeq, ImmunoOncology, Normalization, QualityControl, Software
Version 1.37.0
In Bioconductor since BioC 3.1 (R-3.2) (9 years)
License GPL-2
Depends R (>= 3.2.3), Rsamtools, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg19, IRanges, Biostrings, S4Vectors
System Requirements
See More
Suggests WES.1KG.WUGSC
Linking To
Depends On Me iCNV
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package CODEX_1.37.0.tar.gz
Windows Binary
macOS Binary (x86_64) CODEX_1.37.0.tgz
macOS Binary (arm64) CODEX_1.37.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats