API for aertslab/cisTopic
cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data
| Global functions | |
|---|---|
| .addModels | Source code |
| .distinctColorPalette | Source code |
| .doGREAT | Source code |
| .getColumnNames | Source code |
| .getCtxRegions | Source code |
| .getOneBigWig | Source code |
| .getOverlapRegionsFromCoordinates | Source code |
| .getRowNames | Source code |
| .getScores | Source code |
| .getSignatureRegions | Source code |
| .importRankings | Source code |
| .lda.collapsed.gibbs.sampler_perTopic | Source code |
| .onecisTopicGetCtxCistromes | Source code |
| .plotContinuous | Source code |
| .plotFactor | Source code |
| .predictive.distribution | Source code |
| .runWarpLDA_perTopic | Source code |
| .selectCoordinates | Source code |
| .vertical.image.legend | Source code |
| GREAT | Man page Source code |
| addCellMetadata | Man page Source code |
| addRegionMetadata | Man page Source code |
| annotateRegions | Man page Source code |
| binarizecisTopics | Man page Source code |
| binarizedcisTopicsToCtx | Man page Source code |
| cellData_mel | Man page |
| cellTopicHeatmap | Man page |
| cisTopic | Man page |
| cisTopic-class | Man page |
| counts_mel | Man page |
| createcisTopicObject | Man page Source code |
| createcisTopicObjectFrom10X | Man page Source code |
| createcisTopicObjectFrom10Xmatrix | Man page Source code |
| createcisTopicObjectFromBAM | Man page Source code |
| createcisTopicObjectFromMeth | Man page Source code |
| dm3_CtxRegions | Man page |
| dm6_CtxRegions | Man page |
| getBedFiles | Man page Source code |
| getBigwigFiles | Man page Source code |
| getCistromeEnrichment | Man page Source code |
| getCistromes | Man page Source code |
| getRegionsScores | Man page Source code |
| getSignaturesRegions | Man page Source code |
| hg19_CtxRegions | Man page |
| logLikelihoodByIter | Man page Source code |
| makeBackgroundFeather | Man page Source code |
| mm9_CtxRegions | Man page |
| modelMatSelection | Man page Source code |
| ontologyDotPlot | Man page Source code |
| plotFeatures | Man page Source code |
| predictiveDistribution | Man page Source code |
| renameCells | Man page Source code |
| runCGSModels | Man page Source code |
| runDM | Man page Source code |
| runPCA | Man page Source code |
| runUmap | Man page Source code |
| runWarpLDAModels | Man page Source code |
| runtSNE | Man page Source code |
| scoredRegionsToCtx | Man page Source code |
| selectModel | Man page Source code |
| show | Man page |
| signatureCellEnrichment | Man page Source code |
| signaturesHeatmap | Man page Source code |
| topicSignaturesMatrix | Man page Source code |
| topicsRcisTarget | Man page Source code |
