Files in gerstung-lab/deepSNV
Detection of subclonal SNVs in deep sequencing data.
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
Dockerfile
NAMESPACE
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
data/HIVmix.RData
data/RCC.RData
data/counts.RData
data/phiX.RData
data/pi.RData
data/trueSNVs.RData
inst/CITATION
inst/NEWS
inst/TODO
inst/example/deepSNV-example.R
inst/example/shearwater-example.R
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/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/NAMESPACE.patch
src/Makevars
src/bam2R.cpp
src/betabinom.c
vignettes/deepSNV.Rnw
vignettes/shearwater.Rnw
vignettes/shearwaterML.Rmd
