CODEX
This package is for version 3.17 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: 3.17
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("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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CopyNumberVariation, ExomeSeq, ImmunoOncology, Normalization, QualityControl, Software |
| Version | 1.32.0 |
| 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 | |
| System Requirements | |
| URL |
See More
| 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_1.32.0.tar.gz |
| Windows Binary | CODEX_1.32.0.zip |
| macOS Binary (x86_64) | CODEX_1.32.0.tgz |
| macOS Binary (arm64) | CODEX_1.32.0.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/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.17 | Source Archive |