CODEX-package {CODEX} | R Documentation

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

### Description

CODEX is 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.

### Details

Package: | CODEX
Type: | Package
Version: | 0.99.0
Date: | 2015-01-13
License: | GPL-2

CODEX takes as input the bam files/directories for whole exome sequencing datasets and bed files for exonic positions, returns raw and normalized coverage for each exon, and calls copy number variations with genotyping results.

### Author(s)

Yuchao Jiang <yuchaoj@wharton.upenn.edu>, Nancy R. Zhang

[Package CODEX version 1.22.0 Index]