Package: CODEX
Type: Package
Title: A Normalization and Copy Number Variation Detection Method for
        Whole Exome Sequencing
Version: 1.44.0
Author: Yuchao Jiang, Nancy R. Zhang
Maintainer: Yuchao Jiang <yuchaoj@wharton.upenn.edu>
Description: 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.
License: GPL-2
Depends: R (>= 3.2.3), Rsamtools, GenomeInfoDb,
        BSgenome.Hsapiens.UCSC.hg19, IRanges, Biostrings, S4Vectors
Suggests: WES.1KG.WUGSC
biocViews: ImmunoOncology, ExomeSeq, Normalization, QualityControl,
        CopyNumberVariation
LazyData: yes
git_url: https://git.bioconductor.org/packages/CODEX
git_branch: RELEASE_3_23
git_last_commit: 6ddfc4f
git_last_commit_date: 2026-04-28
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28
NeedsCompilation: no
Packaged: 2026-04-28 21:21:34 UTC; biocbuild
Built: R 4.6.1; ; 2026-07-16 11:13:36 UTC; unix
