CODEX

This package is for version 3.2 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: 3.2

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>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CODEX")

Documentation

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

browseVignettes("CODEX")

Details

Package Archives

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