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✨
DESCRIPTION |NEWS
card.svg |card.png
CODEX/json (API)

# Install 'CODEX' in R:

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

Datasets:

bambedObjDemo - Demo data pre-stored for bambedObj.
coverageObjDemo - Demo data pre-stored for coverageObj.
gcDemo - Demo data pre-stored for GC content.
mapp_ref - Position reference for pre-computed mappability results.
mappability - Pre-computed mappabilities
mappDemo - Demo data pre-stored for mappability.
normObjDemo - Demo data pre-stored for normObj.
qcObjDemo - Demo data pre-stored for qcObj.

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.

immunooncology exomeseq normalization qualitycontrol copynumbervariation

5.36 score 1 packages 38 scripts 484 downloads 72 mentions 9 exports 53 dependencies

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

Target	Result	Time
bioc-checks	ERROR	260
linux-devel-x86_64	NOTE	448
source / vignettes	OK	365
linux-release-x86_64	NOTE	435
macos-release-arm64	NOTE	279
macos-oldrel-arm64	NOTE	280
windows-devel	NOTE	695
windows-release	NOTE	692
windows-oldrel	NOTE	642
wasm-release	OK	224

Exports:choiceofK getbambed getcoverage getgc getmapp normalize normalize2 qc segment

Dependencies:abind askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bitops BSgenome BSgenome.Hsapiens.UCSC.hg19 cigarillo codetools cpp11 crayon curl DelayedArray formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicRanges httr IRanges jsonlite lambda.r lattice Matrix MatrixGenerics matrixStats mime openssl R6 RCurl restfulr Rhtslib rjson Rsamtools rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray SummarizedExperiment sys UCSC.utils XML XVector yaml

Using CODEX

Rendered fromCODEX_vignettes.Rnwusingutils::Sweave

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

Help page	Topics
A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing	CODEX-package CODEX
Demo data pre-stored for bambedObj.	bambedObjDemo
Determine the number of latent factors K.	choiceofK
Demo data pre-stored for coverageObj.	coverageObjDemo
Demo data pre-stored for GC content.	gcDemo
Get bam file directories, sample names, and exonic positions	getbambed
Get depth of coverage from whole exome sequencing	getcoverage
Get GC content for each exonic target	getgc
Get mappability for each exonic target	getmapp
Position reference for pre-computed mappability results.	mapp_ref
Pre-computed mappabilities	mappability
Demo data pre-stored for mappability.	mappDemo
Normalization of read depth from whole exome sequencing	normalize
Normalization of read depth from whole exome sequencing under the case-control setting	normalize2
Demo data pre-stored for normObj.	normObjDemo
Quality control procedure for depth of coverage	qc
Demo data pre-stored for qcObj.	qcObjDemo
Recursive segmentation algorithm for CNV detection and genotyping	segment

Package: CODEX 1.45.0

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

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