Files in navinlabcode/copykit
CopyKit
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS.md
R/AllClasses.R
R/AllGenerics.R
R/calcConsensus.R
R/calcInteger.R
R/calcRatios.R
R/countBreakpoints.R
R/data.R
R/findAneuploidCells.R
R/findClusters.R
R/findOutliers.R
R/findSuggestedK.R
R/findVariableGenes.R
R/inferMrca.R
R/internals.R
R/knnSmooth.R
R/logNorm.R
R/multipcf.R
R/plotAlluvial.R
R/plotConsensusLine.R
R/plotFreq.R
R/plotGeneCopy.R
R/plotHeatmap.R
R/plotMetrics.R
R/plotPca.R
R/plotPhylo.R
R/plotRatio.R
R/plotScree.R
R/plotSuggestedK.R
R/plotUmap.R
R/plotVariableGenes.R
R/runConsensusPhylo.R
R/runCountReads.R
R/runDistMat.R
R/runMetrics.R
R/runPca.R
R/runPhylo.R
R/runSegmentation.R
R/runUmap.R
R/runVarbin.R
R/runVst.R
R/utils-pipe.R
README.Rmd
README.md
_pkgdown.yml
data-raw/genes_granges.R
data-raw/varbin_hg19_chrarm.R
data-raw/varbin_hg19_grangeslist.R
data/copykit_obj_filt_rle.rda
data/copykit_obj_filt_umap.rda
data/copykit_obj_rle.rda
data/hg19_genes.rda
data/hg19_rg.rda
data/hg38_genes.rda
data/hg38_grangeslist.rda
docs/._plotRatioPlotgif.gif
docs/.nojekyll
docs/404.html
docs/LICENSE-text.html
docs/LICENSE.html
docs/authors.html
docs/copykit_workflow.html
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/plotRatioPlotgif.gif
docs/reference/filterCells.html
docs/reference/findClusters.html
docs/reference/geneCopyPlot.html
docs/reference/index.html
docs/reference/pipe.html
docs/reference/plotHeatmap.html
docs/reference/plotUmap.html
docs/reference/readVarbinCNA.html
docs/reference/runDistMat.html
docs/reference/runPhylo.html
docs/reference/runUmap.html
docs/reference/scCNA-class.html
docs/reference/segment_ratios-scCNA-method.html
images/copykit_cheat_sheet_DCM1.png
images/copykit_hexsticker_v2.png
inst/WORDLIST
man/CopyKit-class.Rd
man/calcConsensus.Rd
man/calcInteger.Rd
man/calcRatios.Rd
man/data.Rd
man/dot-countBreakpoints.Rd
man/findAneuploidCells.Rd
man/findClusters.Rd
man/findOutliers.Rd
man/findSuggestedK.Rd
man/findVariableGenes.Rd
man/inferMrca.Rd
man/internals.Rd
man/knnSmooth.Rd
man/logNorm.Rd
man/pipe.Rd
man/plotAlluvial.Rd
man/plotConsensusLine.Rd
man/plotFreq.Rd
man/plotGeneCopy.Rd
man/plotHeatmap.Rd
man/plotMetrics.Rd
man/plotPca.Rd
man/plotPhylo.Rd
man/plotRatio.Rd
man/plotScree.Rd
man/plotSuggestedK.Rd
man/plotUmap.Rd
man/plotVariableGenes.Rd
man/runConsensusPhylo.Rd
man/runCountReads.Rd
man/runDistMat.Rd
man/runMetrics.Rd
man/runPca.Rd
man/runPhylo.Rd
man/runSegmentation.Rd
man/runUmap.Rd
man/runVarbin.Rd
man/runVst.Rd
snakemake_pipelines/bowtie2_markdup/README.md
snakemake_pipelines/bowtie2_markdup/bowtie2_markdup.smk
snakemake_pipelines/bowtie2_markdup/bowtie2_markdup_pairend.smk
snakemake_pipelines/markdup/markdup.smk
tests/spelling.R
tests/testthat.R
tests/testthat/setup.R
tests/testthat/test-dimred-plots.R
tests/testthat/test-plotHeatmap.R
tests/testthat/test-runSegmentation.R
vignettes/.gitignore
vignettes/CopyKit_UserGuide.Rmd
