Man pages for monocle
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
| addCellType | Add a new cell type |
| BEAM | Branched expression analysis modeling (BEAM). |
| branchTest | Test for branch-dependent expression |
| buildBranchCellDataSet | Build a CellDataSet that splits cells among two branches |
| calABCs | Compute the area between curves (ABC) for branch-dependent... |
| calibrate_per_cell_total_proposal | Calibrate_per_cell_total_proposal |
| calILRs | Calculate the Instantaneous Log Ratio between two branches |
| CellDataSet | The CellDataSet class |
| CellDataSet-methods | Methods for the CellDataSet class |
| cellPairwiseDistances | Get the matrix of pairwise distances between cells |
| cellPairwiseDistances-set | Sets the matrix containing distances between each pair of... |
| CellType | The CellType class |
| CellTypeHierarchy | The CellTypeHierarchy class |
| clusterCells | Cluster cells into a specified number of groups based on . |
| clusterGenes | Clusters genes by pseudotime trend. |
| compareModels | Compare model fits |
| detectBifurcationPoint | Calculate divergence times for branch-dependent genes |
| detectGenes | Detects genes above minimum threshold. |
| differentialGeneTest | Test genes for differential expression |
| diff_test_helper | Helper function for parallel differential expression testing |
| dispersionTable | Retrieve a table of values specifying the mean-variance... |
| estimateDispersionsForCellDataSet | Helper function to estimate dispersions |
| estimateSizeFactorsForMatrix | Function to calculate the size factor for the single-cell... |
| estimate_t | Find the most commonly occuring relative expression value in... |
| exportCDS | Export a monocle CellDataSet object to other popular single... |
| extract_good_branched_ordering | Extract a linear ordering of cells from a PQ tree |
| fitModel | Fits a model for each gene in a CellDataSet object. |
| fit_model_helper | Helper function for parallel VGAM fitting |
| genSmoothCurveResiduals | Fit smooth spline curves and return the residuals matrix |
| genSmoothCurves | Fit smooth spline curves and return the response matrix |
| get_classic_muscle_markers | Return the names of classic muscle genes |
| importCDS | Import a seurat or scatter/scran CellDataSet object and... |
| load_HSMM | Build a CellDataSet from the HSMMSingleCell package |
| load_HSMM_markers | Return a CellDataSet of classic muscle genes. |
| load_lung | Build a CellDataSet from the data stored in inst/extdata... |
| markerDiffTable | Test genes for cell type-dependent expression |
| mcesApply | Multicore apply-like function for CellDataSet |
| minSpanningTree | Retrieves the minimum spanning tree generated by Monocle... |
| minSpanningTree-set | Set the minimum spanning tree generated by Monocle during... |
| newCellDataSet | Creates a new CellDateSet object. |
| newCellTypeHierarchy | Classify cells according to a set of markers |
| orderCells | Orders cells according to pseudotime. |
| order_p_node | Return an ordering for a P node in the PQ tree |
| package-deprecated | Plots the minimum spanning tree on cells. This function is... |
| plot_cell_clusters | Plots clusters of cells . |
| plot_cell_trajectory | Plots the minimum spanning tree on cells. |
| plot_clusters | Plots kinetic clusters of genes. |
| plot_coexpression_matrix | Not sure we're ready to release this one quite yet: Plot the... |
| plot_complex_cell_trajectory | Plots the minimum spanning tree on cells. |
| plot_genes_branched_heatmap | Create a heatmap to demonstrate the bifurcation of gene... |
| plot_genes_branched_pseudotime | Plot the branch genes in pseduotime with separate branch... |
| plot_genes_in_pseudotime | Plots expression for one or more genes as a function of... |
| plot_genes_jitter | Plots expression for one or more genes as a jittered, grouped... |
| plot_genes_positive_cells | Plots the number of cells expressing one or more genes as a... |
| plot_genes_violin | Plots expression for one or more genes as a violin plot |
| plot_multiple_branches_heatmap | Create a heatmap to demonstrate the bifurcation of gene... |
| plot_multiple_branches_pseudotime | Create a kinetic curves to demonstrate the bifurcation of... |
| plot_ordering_genes | Plots genes by mean vs. dispersion, highlighting those... |
| plot_pc_variance_explained | Plots the percentage of variance explained by the each... |
| plot_pseudotime_heatmap | Plots a pseudotime-ordered, row-centered heatmap |
| plot_rho_delta | Plots the decision map of density clusters . |
| pq_helper | Recursively builds and returns a PQ tree for the MST |
| reducedDimA | Get the weights needed to lift cells back to high dimensional... |
| reducedDimA-set | Get the weights needed to lift cells back to high dimensional... |
| reducedDimK | Retrieves the the whitening matrix during independent... |
| reducedDimK-set | Sets the the whitening matrix during independent component... |
| reducedDimS | Retrieves the coordinates of each cell in the... |
| reducedDimS-set | Set embedding coordinates of each cell in a CellDataSet. |
| reducedDimW | Get the whitened expression values for a CellDataSet. |
| reducedDimW-set | Sets the whitened expression values for each cell prior to... |
| reduceDimension | Compute a projection of a CellDataSet object into a lower... |
| relative2abs | Transform relative expression values into absolute transcript... |
| residualMatrix | Response values |
| responseMatrix | Calculates response values. |
| selectTopMarkers | Select the most cell type specific markers |
| setOrderingFilter | Marks genes for clustering |
| spike_df | Spike-in transcripts data. |
| vstExprs | Return a variance-stabilized matrix of expression values |
