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

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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
Date of publication
None
Maintainer
Yuchao Jiang <yuchaoj@wharton.upenn.edu>
License
GPL-2
Version
1.6.0

View on Bioconductor

Man pages

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

Files in this package

CODEX/DESCRIPTION
CODEX/NAMESPACE
CODEX/NEWS
CODEX/R
CODEX/R/choiceofK.R
CODEX/R/getbambed.R
CODEX/R/getcoverage.R
CODEX/R/getgc.R
CODEX/R/getmapp.R
CODEX/R/normalize.R
CODEX/R/normalize2.R
CODEX/R/qc.R
CODEX/R/segment.R
CODEX/build
CODEX/build/vignette.rds
CODEX/data
CODEX/data/bambedObjDemo.rda
CODEX/data/coverageObjDemo.rda
CODEX/data/gcDemo.rda
CODEX/data/mappDemo.rda
CODEX/data/mapp_ref.rda
CODEX/data/mappability.rda
CODEX/data/normObjDemo.rda
CODEX/data/qcObjDemo.rda
CODEX/inst
CODEX/inst/doc
CODEX/inst/doc/CODEX_vignettes.R
CODEX/inst/doc/CODEX_vignettes.Rnw
CODEX/inst/doc/CODEX_vignettes.pdf
CODEX/man
CODEX/man/CODEX-package.Rd
CODEX/man/bambedObjDemo.Rd
CODEX/man/choiceofK.Rd
CODEX/man/coverageObjDemo.Rd
CODEX/man/gcDemo.Rd
CODEX/man/getbambed.Rd
CODEX/man/getcoverage.Rd
CODEX/man/getgc.Rd
CODEX/man/getmapp.Rd
CODEX/man/mappDemo.Rd
CODEX/man/mapp_ref.Rd
CODEX/man/mappability.Rd
CODEX/man/normObjDemo.Rd
CODEX/man/normalize.Rd
CODEX/man/normalize2.Rd
CODEX/man/qc.Rd
CODEX/man/qcObjDemo.Rd
CODEX/man/segment.Rd
CODEX/vignettes
CODEX/vignettes/CODEX_vignettes.Rnw