API for compbiomed/celda
CEllular Latent Dirichlet Allocation
| Global functions | |
|---|---|
| .celda_C | Source code |
| .celda_CG | Source code |
| .celda_G | Source code |
| DeconX | Man page Source code |
| available_models | Man page |
| bg.calcLL | Source code |
| cC.calcEMProbZ | Source code |
| cC.calcGibbsProbZ | Source code |
| cC.calcLL | Source code |
| cC.decomposeCounts | Source code |
| cC.reDecomposeCounts | Source code |
| cC.splitZ | Source code |
| cCG.calcLL | Source code |
| cCG.decomposeCounts | Source code |
| cCG.splitY | Source code |
| cCG.splitZ | Source code |
| cD.calcEMDecontamination | Source code |
| cD.calcEMbgDecontamination | Source code |
| cG.calcGibbsProbY | Source code |
| cG.calcLL | Source code |
| cG.decomposeCounts | Source code |
| cG.reDecomposeCounts | Source code |
| cG.splitY | Source code |
| calculateTsne | Source code |
| celda | Man page Source code |
| celda.C.mod | Man page |
| celda.C.sim | Man page |
| celda.CG.grid.search.res | Man page |
| celda.CG.mod | Man page |
| celda.CG.sim | Man page |
| celda.G.mod | Man page |
| celda.G.sim | Man page |
| celdaGridSearch | Man page Source code |
| celdaHeatmap | Man page Source code |
| celdaHeatmap.celda_C | Man page Source code |
| celdaHeatmap.celda_CG | Man page Source code |
| celdaHeatmap.celda_G | Man page Source code |
| celdaProbabilityMap | Man page Source code |
| celdaProbabilityMap.celda_C | Man page Source code |
| celdaProbabilityMap.celda_CG | Man page Source code |
| celdaTsne | Man page Source code |
| celdaTsne.celda_C | Man page Source code |
| celdaTsne.celda_CG | Man page Source code |
| celdaTsne.celda_G | Man page Source code |
| celda_C | Man page Source code |
| celda_CG | Man page Source code |
| celda_G | Man page Source code |
| checkCounts.decon | Source code |
| checkParameters.decon | Source code |
| clusterProbability | Man page Source code |
| clusterProbability.celda_C | Man page Source code |
| clusterProbability.celda_CG | Man page Source code |
| clusterProbability.celda_G | Man page Source code |
| cluster_mat | Source code |
| colSumByGroup | Source code |
| colSumByGroup.numeric | Source code |
| colSumByGroupChange | Source code |
| compareCountMatrix | Man page Source code |
| completeLogLikelihood | Man page Source code |
| contamination.sim | Man page |
| convert_annotations | Source code |
| cosine | Source code |
| cosineDist | Source code |
| decon.calcLL | Source code |
| differentialExpression | Man page Source code |
| distinct_colors | Man page Source code |
| draw_annotation_legend | Source code |
| draw_annotation_names | Source code |
| draw_annotations | Source code |
| draw_colnames | Source code |
| draw_dendrogram | Source code |
| draw_legend | Source code |
| draw_main | Source code |
| draw_matrix | Source code |
| draw_rownames | Source code |
| eigenMatMultInt | Man page Source code |
| factorizeMatrix | Man page Source code |
| factorizeMatrix.celda_C | Man page Source code |
| factorizeMatrix.celda_CG | Man page Source code |
| factorizeMatrix.celda_G | Man page Source code |
| fastNormProp | Man page Source code |
| fastNormPropLog | Man page Source code |
| fastNormPropSqrt | Man page Source code |
| featureModuleLookup | Man page Source code |
| featureModuleLookup.celda_C | Man page Source code |
| featureModuleLookup.celda_CG | Man page Source code |
| featureModuleLookup.celda_G | Man page Source code |
| featureModuleTable | Man page Source code |
| finalLogLikelihood | Man page Source code |
| find_coordinates | Source code |
| find_gaps | Source code |
| generate_annotation_colours | Source code |
| generate_breaks | Source code |
| heatmap_motor | Source code |
| hellingerDist | Source code |
| identity2 | Source code |
| initialize.cluster | Source code |
| is.na2 | Source code |
| kmeans_pheatmap | Source code |
| lo | Source code |
| logLikelihood | Man page Source code |
| logLikelihood.celda_C | Man page Source code |
| logLikelihood.celda_CG | Man page Source code |
| logLikelihood.celda_G | Man page Source code |
| logMessages | Source code |
| moduleHeatmap | Man page Source code |
| normalizeCounts | Man page Source code |
| normalizeLogProbs | Source code |
| perplexity | Man page Source code |
| perplexity.celda_C | Man page Source code |
| perplexity.celda_CG | Man page Source code |
| perplexity.celda_G | Man page Source code |
| plotDimReduceCluster | Man page Source code |
| plotDimReduceFeature | Man page Source code |
| plotDimReduceGrid | Man page Source code |
| plotDimReduceModule | Man page Source code |
| plotGridSearchPerplexity | Man page Source code |
| plotGridSearchPerplexity.celda_C | Man page Source code |
| plotGridSearchPerplexity.celda_CG | Man page Source code |
| plotGridSearchPerplexity.celda_G | Man page Source code |
| plotHeatmap | Man page Source code |
| processCellLabels | Source code |
| processCounts | Source code |
| processSampleLabels | Source code |
| rdirichlet | Source code |
| recodeClusterY | Man page Source code |
| recodeClusterZ | Man page Source code |
| recursive.splitY | Source code |
| recursive.splitZ | Source code |
| reorder.celda_C | Source code |
| reorder.celda_CG | Source code |
| reorder.celda_G | Source code |
| resampleCountMatrix | Source code |
| resamplePerplexity | Man page Source code |
| rowSumByGroup | Source code |
| rowSumByGroup.numeric | Source code |
| rowSumByGroupChange | Source code |
| runParams | Man page Source code |
| sample.cells | Man page |
| sample.ll | Source code |
| scale_colours | Source code |
| scale_mat | Source code |
| scale_rows | Source code |
| scale_vec_colours | Source code |
| selectBestModel | Man page Source code |
| semi_pheatmap | Man page Source code |
| simulateCells | Man page Source code |
| simulateCells.celda_C | Man page Source code |
| simulateCells.celda_CG | Man page Source code |
| simulateCells.celda_G | Man page Source code |
| simulateObservedMatrix | Man page Source code |
| spearmanDist | Source code |
| subsetCeldaList | Man page Source code |
| topRank | Man page Source code |
| validateCounts | Source code |
| violinPlot | Man page Source code |
| vplayout | Source code |
