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CODEX

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


Bioconductor version: Release (3.18)

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 "4.3") and enter:


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

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

Details

biocViews CopyNumberVariation, ExomeSeq, ImmunoOncology, Normalization, QualityControl, Software
Version 1.34.0
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
Imports
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Suggests WES.1KG.WUGSC
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Package Archives

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

Source Package CODEX_1.34.0.tar.gz
Windows Binary CODEX_1.34.0.zip
macOS Binary (x86_64) CODEX_1.34.0.tgz
macOS Binary (arm64) CODEX_1.34.0.tgz
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/
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