Man pages for aertslab/cisTopic
cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data
| addCellMetadata | Add cells metadata to a cisTopic object |
| addRegionMetadata | Add regions metadata to a cisTopic object |
| annotateRegions | annotateRegions |
| binarizecisTopics | Binarize cisTopic |
| binarizedcisTopicsToCtx | binarizedcisTopicsToCtx |
| cellData_mel | Cell data from simulated single cell epigenomes from 5 bulk... |
| cellTopicHeatmap | Cell-cisTopic distribution heatmap |
| cisTopic | The cisTopic Class |
| counts_mel | Cell data from simulated single cell epigenomes from 5 bulk... |
| createcisTopicObject | Initialize and setup the cisTopic object |
| createcisTopicObjectFrom10X | Initialize and setup the cisTopic object starting from... |
| createcisTopicObjectFrom10Xmatrix | Initialize and setup the cisTopic object starting from... |
| createcisTopicObjectFromBAM | Initialize and setup the cisTopic object starting from bam... |
| createcisTopicObjectFromMeth | Initialize and setup the cisTopic object starting from... |
| dm3_CtxRegions | Data frame containing the mapping from ctx regions to genome... |
| dm6_CtxRegions | Data frame containing the mapping from ctx regions to genome... |
| getBedFiles | getBedFiles |
| getBigwigFiles | getBigwigFiles |
| getCistromeEnrichment | getCistromeEnrichment |
| getCistromes | getCistromes |
| getRegionsScores | Get region scores |
| getSignaturesRegions | getSignaturesRegions |
| GREAT | GREAT |
| hg19_CtxRegions | Data frame containing the mapping from ctx regions to genome... |
| logLikelihoodByIter | Plots log likelihood in the models per iteration. |
| makeBackgroundFeather | makeBackgroundFeather |
| mm9_CtxRegions | Data frame containing the mapping from ctx regions to genome... |
| modelMatSelection | Retrieve normalised topic-cell and region-topic assignments |
| ontologyDotPlot | ontologyDotPlot |
| plotFeatures | Plot features (cells or regions) based on dimensionality... |
| predictiveDistribution | Probability of each region in each cell in the data set. |
| renameCells | Rename cells in a cisTopic object |
| runCGSModels | Run Latent Dirichlet Allocation with a Collapsed Gibbs... |
| runDM | Calculate Diffusion Components on the cell-cisTopic... |
| runPCA | Calculate Principal Components on the cell-cisTopic... |
| runtSNE | Run tSNE on the cell-cisTopic/region-cisTopic distributions |
| runUmap | Run umap on the cell-cisTopic/region-cisTopic distributions |
| runWarpLDAModels | Run Latent Dirichlet Allocation with WarpLDA in a cisTopic... |
| scoredRegionsToCtx | scoredRegionsToCtx |
| selectModel | Model selection based on log likelihood |
| show | Show method for cisTopic |
| signatureCellEnrichment | signatureCellEnrichment |
| signaturesHeatmap | signaturesHeatmap |
| topicSignaturesMatrix | topicSignaturesMatrix |
| topicsRcisTarget | topicsRcisTarget |
