Files in deepSNV
Detection of subclonal SNVs in deep sequencing data.

DESCRIPTION
NAMESPACE
R
R/betabinom.R R/deepSNV-class.R R/deepSNV-experimental.R R/deepSNV-functions.R R/deepSNV-generics.R R/deepSNV-methods.R R/deepSNV-misc.R R/deepSNV-package.R R/shearwater-functions.R R/shearwaterML.R README.md
build
build/vignette.rds
configure
configure.ac
data
data/HIVmix.RData
data/RCC.RData
data/counts.RData
data/phiX.RData
data/pi.RData
data/trueSNVs.RData
inst
inst/CITATION
inst/NEWS
inst/TODO
inst/doc
inst/doc/deepSNV.R
inst/doc/deepSNV.Rnw
inst/doc/deepSNV.pdf inst/doc/shearwater.R
inst/doc/shearwater.Rnw
inst/doc/shearwater.pdf inst/doc/shearwaterML.R inst/doc/shearwaterML.Rmd
inst/doc/shearwaterML.html
inst/example
inst/example/deepSNV-example.R inst/example/shearwater-example.R
inst/extdata
inst/extdata/control.bam
inst/extdata/control.bam.bai
inst/extdata/deepSNV.vcf
inst/extdata/shearwater.vcf
inst/extdata/shearwater2.vcf
inst/extdata/shearwaterML.vcf
inst/extdata/test.bam
inst/extdata/test.bam.bai
man
man/Extract-methods.Rd man/RCC.Rd man/RF.Rd man/bam2R.Rd man/betabinLRT.Rd man/bf2Vcf.Rd man/consensusSequence-methods.Rd man/control-methods.Rd man/coordinates-methods.Rd man/counts.Rd man/dbetabinom.Rd man/deepSNV-class.Rd man/deepSNV-methods.Rd man/deepSNV-package.Rd man/estimateDirichlet-methods.Rd man/estimateDispersion-methods.Rd man/estimateRho.Rd man/loadAllData.Rd man/makePrior.Rd man/manhattanPlot.Rd man/mcChunk.Rd man/normalize-methods.Rd man/p.combine.Rd man/p.val-methods.Rd man/pbetabinom.Rd man/phiX.Rd man/pi.Rd man/plot.deepSNV.Rd man/qvals2Vcf.Rd man/repeatMask-methods.Rd man/shearwater.Rd man/show-deepSNV-method.Rd man/summary-methods.Rd man/test-methods.Rd man/trueSNVs.Rd
patches
patches/NAMESPACE.patch
src
src/Makevars
src/Makevars.common
src/Makevars.in
src/Makevars.win
src/bam2R.cpp
src/betabinom.c
vignettes
vignettes/deepSNV.Rnw
vignettes/shearwater.Rnw
vignettes/shearwaterML.Rmd
deepSNV documentation built on May 31, 2017, 11:17 a.m.