CODEX

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 (3.21)

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>

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

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("CODEX")

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

Documentation

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

browseVignettes("CODEX")

Using CODEX	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CopyNumberVariation, ExomeSeq, ImmunoOncology, Normalization, QualityControl, Software
Version	1.39.0
In Bioconductor since	BioC 3.1 (R-3.2) (9.5 years)
License	GPL-2
Depends	R (>= 3.2.3), Rsamtools, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg19, IRanges, Biostrings, S4Vectors
Imports
System Requirements
URL

Suggests	WES.1KG.WUGSC
Linking To
Enhances
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_1.39.0.tar.gz
Windows Binary (x86_64)	CODEX_1.39.0.zip
macOS Binary (x86_64)	CODEX_1.39.0.tgz
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/CODEX
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CODEX
Bioc Package Browser	https://code.bioconductor.org/browse/CODEX/
Package Short Url	https://bioconductor.org/packages/CODEX/
Package Downloads Report	Download Stats