├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── R ├── Annotation.R ├── BasicTopicOperations.R ├── InitializecisTopic.R ├── OverlapcisTopic.R ├── PlotCells.R ├── RcisTarget.R ├── RunModels.R ├── cellData_mel.R ├── cisTopic.R ├── counts_mel.R └── data_exports.R ├── README.md ├── cistopic_singularity.def ├── data ├── cellData_mel.RData ├── counts_mel.RData ├── dm3_CtxRegions.RData ├── dm6_CtxRegions.RData ├── hg19_CtxRegions.RData └── mm9_CtxRegions.RData ├── inst └── examples │ └── cisTopicObject_melanoma.Rds ├── man ├── GREAT.Rd ├── addCellMetadata.Rd ├── addRegionMetadata.Rd ├── annotateRegions.Rd ├── binarizecisTopics.Rd ├── binarizedcisTopicsToCtx.Rd ├── cellData_mel.Rd ├── cellTopicHeatmap.Rd ├── cisTopic.Rd ├── counts_mel.Rd ├── createcisTopicObject.Rd ├── createcisTopicObjectFrom10X.Rd ├── createcisTopicObjectFrom10Xmatrix.Rd ├── createcisTopicObjectFromBAM.Rd ├── createcisTopicObjectFromMeth.Rd ├── dm3_CtxRegions.Rd ├── dm6_CtxRegions.Rd ├── getBedFiles.Rd ├── getBigwigFiles.Rd ├── getCistromeEnrichment.Rd ├── getCistromes.Rd ├── getRegionsScores.Rd ├── getSignaturesRegions.Rd ├── hg19_CtxRegions.Rd ├── logLikelihoodByIter.Rd ├── makeBackgroundFeather.Rd ├── mm9_CtxRegions.Rd ├── modelMatSelection.Rd ├── ontologyDotPlot.Rd ├── plotFeatures.Rd ├── predictiveDistribution.Rd ├── renameCells.Rd ├── runCGSModels.Rd ├── runDM.Rd ├── runPCA.Rd ├── runUmap.Rd ├── runWarpLDAModels.Rd ├── runtSNE.Rd ├── scoredRegionsToCtx.Rd ├── selectModel.Rd ├── show.Rd ├── signatureCellEnrichment.Rd ├── signaturesHeatmap.Rd ├── topicSignaturesMatrix.Rd └── topicsRcisTarget.Rd └── vignettes ├── 10X_workflow.Rmd ├── 10X_workflow.html ├── CompleteAnalysis.Rmd ├── CompleteAnalysis.html ├── Runningwithmm10andhg38.Rmd ├── Runningwithmm10andhg38.html ├── WarpLDA_10X_workflow.Rmd ├── WarpLDA_10X_workflow.html ├── WarpLDA_CompleteAnalysis.Rmd └── WarpLDA_CompleteAnalysis.html /.gitignore: -------------------------------------------------------------------------------- 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