SomatiCA: SomatiCA: identifying, characterizing, and quantifying somatic copy number aberrations from cancer genome sequencing

SomatiCA is a software suite that is capable of identifying, characterizing, and quantifying somatic CNAs from cancer genome sequencing. First, it uses read depths and lesser allele frequencies (LAF) from mapped short sequence reads to segment the genome and identify candidate CNAs. Second, SomatiCA estimates the admixture rate from the relative copy-number profile of tumor-normal pair by a Bayesian finite mixture model. Third, SomatiCA quantifies absolute somatic copy-number and subclonality for each genomic segment to guide its characterization. Results from SomatiCA can be further integrated with single nucleotide variations (SNVs) to get a better understanding of the tumor evolution.

AuthorMengjie Chen <mengjie.chen@yale.edu>, Hongyu Zhao <hongyu.zhao@yale.edu>
Date of publicationNone
MaintainerMengjie Chen <mengjie.chen@yale.edu>
LicenseGPL (>=2)
Version2.2.1

View on Bioconductor

Files in this package

SomatiCA/DESCRIPTION
SomatiCA/NAMESPACE
SomatiCA/R
SomatiCA/R/AllGeneric.R
SomatiCA/R/GCbiasRemoval.R
SomatiCA/R/GCcount.R
SomatiCA/R/MergeSegment.R
SomatiCA/R/SomatiCA-internal.R
SomatiCA/R/SomatiCAFormat.R
SomatiCA/R/SomatiCAUsersGuide.R
SomatiCA/R/SomatiCApipe.R
SomatiCA/R/admixtureRate.R
SomatiCA/R/collapse.R
SomatiCA/R/copynumberCorrected.R
SomatiCA/R/denoise.R
SomatiCA/R/larsCBSsegment.R
SomatiCA/R/plotSegment.R
SomatiCA/R/plotSubclonality.R
SomatiCA/R/refineSegment.R
SomatiCA/R/segmentGCbiasRemoval.R
SomatiCA/R/somaticRatio.R
SomatiCA/R/subclonality.R
SomatiCA/R/zzz.R
SomatiCA/build
SomatiCA/build/vignette.rds
SomatiCA/data
SomatiCA/data/GCcontent.rda
SomatiCA/data/datalist
SomatiCA/data/segwithratio.rda
SomatiCA/inst
SomatiCA/inst/CITATION
SomatiCA/inst/doc
SomatiCA/inst/doc/SomatiCA.R
SomatiCA/inst/doc/SomatiCA.Rnw
SomatiCA/inst/doc/SomatiCA.pdf
SomatiCA/inst/doc/SomatiCAUserGuide.pdf
SomatiCA/man
SomatiCA/man/GCbiasRemoval.Rd SomatiCA/man/GCcontent.Rd SomatiCA/man/GCcount.Rd SomatiCA/man/MergeSegment.Rd SomatiCA/man/SomatiCA-package.Rd SomatiCA/man/SomatiCAFormat-methods.Rd SomatiCA/man/SomatiCAUsersGuide.Rd SomatiCA/man/SomatiCApipe.Rd SomatiCA/man/admixtureRate.Rd SomatiCA/man/collapse.Rd SomatiCA/man/copynumberCorrected.Rd SomatiCA/man/denoise.Rd SomatiCA/man/larsCBSsegment.Rd SomatiCA/man/plotSegment.Rd SomatiCA/man/plotSubclonality.Rd SomatiCA/man/refineSegment.Rd SomatiCA/man/segmentGCbiasRemoval.Rd SomatiCA/man/segwithratio.Rd SomatiCA/man/somaticRatio.Rd SomatiCA/man/subclonality.Rd
SomatiCA/vignettes
SomatiCA/vignettes/SomatiCA.Rnw

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