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 SequencingBioconductor version: Development (3.22)
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, entercitation("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.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CODEX")Follow Installation instructions to use this package in your R session.
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