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/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

navinlabcode/copykit documentation built on Sept. 22, 2023, 9:16 a.m.