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.

AuthorYuchao Jiang, Nancy R. Zhang
Date of publicationNone
MaintainerYuchao Jiang <yuchaoj@wharton.upenn.edu>
LicenseGPL-2
Version1.6.0

View on Bioconductor

Files

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

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