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
Config/pak/sysreqs: make libbz2-dev liblzma-dev libxml2-dev libssl-dev
        xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 12:40:22 UTC
RemoteUrl: https://github.com/bioc/CODEX
RemoteRef: RELEASE_3_23
RemoteSha: 6ddfc4ffeb9b034cae3e52cc3430a04e0cd1a312
NeedsCompilation: no
Packaged: 2026-04-29 20:43:41 UTC; root
Built: R 4.6.0; ; 2026-04-29 20:54:19 UTC; windows
