API for monocle
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
| Global functions | |
|---|---|
| BEAM | Man page Source code |
| CellDataSet | Man page |
| CellDataSet,ANY,ANY-method | Man page Man page Man page Man page |
| CellDataSet-class | Man page |
| CellDataSet-methods | Man page |
| CellType | Man page |
| CellType-class | Man page |
| CellTypeHierarchy | Man page |
| CellTypeHierarchy-class | Man page |
| `cellPairwiseDistances<-` | Source code |
| `minSpanningTree<-` | Source code |
| `reducedDimA<-` | Source code |
| `reducedDimK<-` | Source code |
| `reducedDimS<-` | Source code |
| `reducedDimW<-` | Source code |
| addCellType | Man page Source code |
| branchTest | Man page Source code |
| buildBranchCellDataSet | Man page Source code |
| calABCs | Man page Source code |
| calILRs | Man page |
| calculateMarkerSpecificity | Man page Source code |
| calculate_NB_dispersion_hint | Source code |
| calculate_QP_dispersion_hint | Source code |
| calibrate_per_cell_total_proposal | Man page Source code |
| cellPairwiseDistances | Man page Source code |
| cellPairwiseDistances<- | Man page |
| checkSizeFactors | Source code |
| classifyCells | Man page Source code |
| classifyCellsHelperCds | Source code |
| classifyCellsHelperCell | Source code |
| clusterCells | Man page Source code |
| clusterGenes | Man page Source code |
| compareModels | Man page Source code |
| cth_classifier_cds | Source code |
| cth_classifier_cell | Source code |
| detectBifurcationPoint | Man page Source code |
| detectGenes | Man page Source code |
| diff_test_helper | Man page Source code |
| differentialGeneTest | Man page Source code |
| disp_calc_helper_NB | Source code |
| dispersionTable | Man page Source code |
| dmode | Source code |
| estimateDispersions,CellDataSet-method | Man page |
| estimateDispersionsForCellDataSet | Man page Source code |
| estimateSizeFactors,CellDataSet-method | Man page |
| estimateSizeFactorsForDenseMatrix | Source code |
| estimateSizeFactorsForMatrix | Man page Source code |
| estimateSizeFactorsForSparseMatrix | Source code |
| estimate_t | Man page Source code |
| exportCDS | Man page Source code |
| extract_good_branched_ordering | Man page |
| fitModel | Man page Source code |
| fit_model_helper | Man page Source code |
| genSmoothCurveResiduals | Man page Source code |
| genSmoothCurves | Man page Source code |
| get_classic_muscle_markers | Man page Source code |
| importCDS | Man page Source code |
| isSparseMatrix | Source code |
| jaccard_coeff | Source code |
| load_HSMM | Man page Source code |
| load_HSMM_markers | Man page Source code |
| load_lung | Man page Source code |
| makeprobs | Source code |
| makeprobsvec | Source code |
| markerDiffTable | Man page |
| mcesApply | Man page Source code |
| minSpanningTree | Man page Source code |
| minSpanningTree<- | Man page |
| monocle_theme_opts | Source code |
| newCellDataSet | Man page Source code |
| newCellTypeHierarchy | Man page Source code |
| norm_kb | Source code |
| opt_norm_kb | Source code |
| opt_norm_t | Source code |
| orderCells | Man page |
| order_p_node | Man page |
| parametricDispersionFit | Source code |
| plot_cell_clusters | Man page |
| plot_cell_trajectory | Man page Source code |
| plot_clusters | Man page |
| plot_coexpression_matrix | Man page |
| plot_complex_cell_trajectory | Man page |
| plot_genes_branched_heatmap | Man page |
| plot_genes_branched_pseudotime | Man page |
| plot_genes_in_pseudotime | Man page |
| plot_genes_jitter | Man page |
| plot_genes_positive_cells | Man page |
| plot_genes_violin | Man page |
| plot_multiple_branches_heatmap | Man page |
| plot_multiple_branches_pseudotime | Man page |
| plot_ordering_genes | Man page |
| plot_pc_variance_explained | Man page |
| plot_pseudotime_heatmap | Man page |
| plot_rho_delta | Man page |
| plot_spanning_tree | Man page |
| pq_helper | Man page |
| reduceDimension | Man page |
| reducedDimA | Man page Source code |
| reducedDimA<- | Man page |
| reducedDimK | Man page Source code |
| reducedDimK<- | Man page |
| reducedDimS | Man page Source code |
| reducedDimS<- | Man page |
| reducedDimW | Man page Source code |
| reducedDimW<- | Man page |
| relative2abs | Man page Source code |
| residualMatrix | Man page Source code |
| responseMatrix | Man page Source code |
| run_pca | Source code |
| scale_pseudotime | Source code |
| selectTopMarkers | Man page Source code |
| setOrderingFilter | Man page |
| shannon.entropy | Source code |
| sizeFactors,CellDataSet-method | Man page |
| sizeFactors<-,CellDataSet,numeric-method | Man page |
| smartEsApply | Source code |
| sparseApply | Source code |
| spike_df | Man page |
| vstExprs | Man page Source code |
