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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SomatiCA")
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

Functions

admixtureRate Man page
collapse Man page
copynumberCorrected Man page
denoise Man page
GCbiasRemoval Man page
GCcontent Man page
GCcount Man page
larsCBSsegment Man page
MergeSegment Man page
plotSegment Man page
plotSubclonality Man page
refineSegment Man page
segmentGCbiasRemoval Man page
segwithratio Man page
SomatiCA Man page
SomatiCAFormat Man page
SomatiCAFormat,character-method Man page
SomatiCAFormat,data.frame-method Man page
SomatiCAFormat,GRanges-method Man page
SomatiCAFormat-methods Man page
SomatiCA-package Man page
SomatiCApipe Man page
SomatiCAUsersGuide Man page
somaticRatio Man page
subclonality Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.