Files in JEFworks/HoneyBADGER
HMM-integrated Bayesian approach for detecting CNV and LOH events using single-cell RNA-seq data
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
R/HoneyBADGER.R
R/HoneyBADGER_allele.R
R/HoneyBADGER_comb.R
R/HoneyBADGER_gexp.R
R/clonal_deletion_detection.R
R/data.R
R/external.R
R/prepareData.R
README.md
data/cov.sc.rda
data/gexp.rda
data/r.rda
data/ref.rda
docs/Getting_Started.md
docs/Integrating.md
docs/Preparing_Data.md
docs/_config.yml
docs/_layouts/default.html
docs/_sass/fonts.scss
docs/_sass/jekyll-theme-minimal.scss
docs/_sass/rouge-github.scss
docs/assets/css/style.scss
docs/assets/fonts/Noto-Sans-700/Noto-Sans-700.eot
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docs/assets/img/approach.png
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docs/assets/img/integration.png
docs/assets/img/logo.png
docs/assets/js/scale.fix.js
docs/favicon.ico
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docs/figure/Integrating/unnamed-chunk-8-2.png
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docs/index.md
inst/CITATION
inst/ExAC/ExAC_chr1.RData
inst/ExAC/ExAC_chr10.RData
inst/ExAC/ExAC_chr11.RData
inst/ExAC/ExAC_chr12.RData
inst/ExAC/ExAC_chr13.RData
inst/ExAC/ExAC_chr14.RData
inst/ExAC/ExAC_chr15.RData
inst/ExAC/ExAC_chr16.RData
inst/ExAC/ExAC_chr17.RData
inst/ExAC/ExAC_chr18.RData
inst/ExAC/ExAC_chr19.RData
inst/ExAC/ExAC_chr2.RData
inst/ExAC/ExAC_chr20.RData
inst/ExAC/ExAC_chr21.RData
inst/ExAC/ExAC_chr22.RData
inst/ExAC/ExAC_chr3.RData
inst/ExAC/ExAC_chr4.RData
inst/ExAC/ExAC_chr5.RData
inst/ExAC/ExAC_chr6.RData
inst/ExAC/ExAC_chr7.RData
inst/ExAC/ExAC_chr8.RData
inst/ExAC/ExAC_chr9.RData
inst/ExAC/README.md
inst/bug/combinedModel.bug
inst/bug/expressionModel.bug
inst/bug/snpModel.bug
man/HoneyBADGER-class.Rd
man/HoneyBADGER_calcAlleleCnvBoundaries.Rd
man/HoneyBADGER_calcAlleleCnvProb.Rd
man/HoneyBADGER_calcCombCnvProb.Rd
man/HoneyBADGER_calcGexpCnvBoundaries.Rd
man/HoneyBADGER_calcGexpCnvProb.Rd
man/HoneyBADGER_plotAlleleProfile.Rd
man/HoneyBADGER_plotGexpProfile.Rd
man/HoneyBADGER_plotSmoothedAlleleProfile.Rd
man/HoneyBADGER_retestIdentifiedCnvs.Rd
man/HoneyBADGER_setAlleleMats.Rd
man/HoneyBADGER_setGeneFactors.Rd
man/HoneyBADGER_setGexpDev.Rd
man/HoneyBADGER_setGexpMats.Rd
man/HoneyBADGER_setMvFit.Rd
man/HoneyBADGER_summarizeResults.Rd
man/HoneyBADGER_visualizeResults.Rd
man/calcAlleleCnvBoundaries.Rd
man/calcAlleleCnvProb.Rd
man/calcCombCnvProb.Rd
man/calcGexpCnvBoundaries.Rd
man/calcGexpCnvProb.Rd
man/cov.sc.Rd
man/getAlleleCount.Rd
man/getCellAlleleCount.Rd
man/getCoverage.Rd
man/getHetRate.Rd
man/getSnpMats.Rd
man/getSnpMats10X.Rd
man/gexp.Rd
man/isHet.Rd
man/isHetAlt.Rd
man/plotAlleleProfile.Rd
man/plotGexpProfile.Rd
man/r.Rd
man/ref.Rd
man/setAlleleMats.Rd
man/setGeneFactors.Rd
man/setGexpDev.Rd
man/setGexpMats.Rd
man/setMvFit.Rd
man/trimSnps.Rd
vignettes/Getting_Started.Rmd
vignettes/Integrating.Rmd
vignettes/Preparing_Data.Rmd
vignettes/figure/unnamed-chunk-11-1.png
vignettes/figure/unnamed-chunk-12-1.png
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