Package: CODEX 1.45.0

Yuchao Jiang

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

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.

Authors:Yuchao Jiang, Nancy R. Zhang

CODEX_1.45.0.tar.gz
CODEX_1.45.0.zip(r-4.7)CODEX_1.45.0.zip(r-4.6)CODEX_1.45.0.zip(r-4.5)
CODEX_1.45.0.tgz(r-4.6-any)CODEX_1.45.0.tgz(r-4.5-any)
CODEX_1.45.0.tar.gz(r-4.7-any)CODEX_1.45.0.tar.gz(r-4.6-any)
CODEX_1.45.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
CODEX/json (API)
NEWS

# Install 'CODEX' in R:
install.packages('CODEX', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:

On BioConductor:CODEX-1.45.0(bioc 3.24)CODEX-1.44.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncologyexomeseqnormalizationqualitycontrolcopynumbervariation

5.45 score 1 packages 47 scripts 491 downloads 72 mentions 9 exports 53 dependencies

Last updated from:892afc3300. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR245
linux-devel-x86_64NOTE438
source / vignettesOK353
linux-release-x86_64NOTE446
macos-release-arm64NOTE477
macos-oldrel-arm64NOTE297
windows-develNOTE691
windows-releaseNOTE732
windows-oldrelNOTE634
wasm-releaseOK204

Exports:choiceofKgetbambedgetcoveragegetgcgetmappnormalizenormalize2qcsegment

Dependencies:abindaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomeBSgenome.Hsapiens.UCSC.hg19cigarillocodetoolscpp11crayoncurlDelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicRangeshttrIRangesjsonlitelambda.rlatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6RCurlrestfulrRhtslibrjsonRsamtoolsrtracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsysUCSC.utilsXMLXVectoryaml

Using CODEX

Rendered fromCODEX_vignettes.Rnwusingutils::Sweaveon May 30 2026.

Last update: 2018-08-30
Started: 2014-12-13