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

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.

Package details

AuthorYuchao Jiang, Nancy R. Zhang
Bioconductor views CopyNumberVariation ExomeSeq ImmunoOncology Normalization QualityControl
MaintainerYuchao Jiang <>
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
if (!requireNamespace("BiocManager", quietly = TRUE))


Try the CODEX package in your browser

Any scripts or data that you put into this service are public.

CODEX documentation built on Nov. 8, 2020, 8:22 p.m.