Man pages for cole-trapnell-lab/monocle3
Clustering, Differential Expression, and Trajectory Analysis for Single-Cell RNA-Seq
| aggregate_gene_expression | Creates a matrix with aggregated expression values for... |
| align_cds | Align cells from different groups within a cds |
| align_transform | Apply an alignment transform model to a cell_data_set. |
| calc_principal_graph | Function to automatically learn the structure of data by... |
| cell_data_set | The cell_data_set class |
| cell_data_set-methods | Methods for the cell_data_set class |
| choose_cells | Choose cells interactively to subset a cds |
| choose_graph_segments | Choose cells along the path of a principal graph |
| clear_cds_slots | Clear CDS slots |
| cluster_cells | Cluster cells using Louvain/Leiden community detection |
| clusters | Generic to extract clusters from CDS object |
| clusters-cell_data_set-method | Method to extract clusters from CDS object |
| coefficient_table | Extract coefficient table from a fit_models result. |
| combine_cds | Combine a list of cell_data_set objects |
| compare_models | Compare goodness of fit of two models. |
| detect_genes | Detects genes above minimum threshold. |
| estimate_size_factors | Function to calculate size factors for single-cell RNA-seq... |
| evaluate_fits | Evaluate fit of model objects. |
| exprs | Generic to access cds count matrix |
| exprs-cell_data_set-method | Method to access cds count matrix |
| fData | Generic to access cds rowData table |
| fData-cell_data_set-method | Method to access cds rowData table |
| fData-set | Generic to set cds rowData table |
| fData-set-cell_data_set-method | Method to set cds rowData table |
| find_gene_modules | Cluster genes into modules that are co-expressed across... |
| fit_models | Fits a model for each gene in a cell_data_set object. |
| fix_missing_cell_labels | Replace NA cell column data values left after running... |
| generate_centers | Function to reproduce the behavior of eye function in matlab |
| generate_garnett_marker_file | Generate a Garnett marker file from top_markers output. |
| get_citations | Access citations for methods used during analysis. |
| get_genome_in_matrix_path | Get a genome from Cell Ranger output |
| graph_test | Test genes for differential expression based on the low... |
| identity_table | Report matrix and model identity information. |
| learn_graph | Learn principal graph from the reduced dimension space using... |
| load_a549 | Build a small cell_data_set. |
| load_cellranger_data | Load data from the 10x Genomics Cell Ranger pipeline |
| load_mm_data | Load data from matrix market format files. |
| load_monocle_objects | Load a full Monocle3 cell_data_set. |
| load_mtx_data | Load data from matrix market format |
| load_transform_models | Load transform models into a cell_data_set. |
| load_worm_embryo | Build a cell_data_set from C. elegans embryo data. |
| load_worm_l2 | Build a cell_data_set from C. elegans L2 data. |
| make_cds_nn_index | Make and store a nearest neighbor index in the cell_data_set. |
| make_nn_index | Make a nearest neighbor index. |
| mc_es_apply | Multicore apply-like function for cell_data_set |
| model_predictions | Predict values of new data using fit_models model. |
| new_cell_data_set | Create a new cell_data_set object. |
| normalized_counts | Return a size-factor normalized and (optionally)... |
| order_cells | Orders cells according to pseudotime. |
| partitions | Generic to extract partitions from CDS object |
| partitions-cell_data_set-method | Method to extract partitions from CDS object |
| pData | Generic to access cds colData table |
| pData-cell_data_set-method | Method to access cds colData table |
| pData-set | Generic to set cds colData table |
| pData-set-cell_data_set-method | Method to set cds colData table |
| plot_cells | Plots the cells along with their trajectories. |
| plot_cells_3d | Plot a dataset and trajectory in 3 dimensions |
| plot_genes_by_group | Create a dot plot to visualize the mean gene expression and... |
| plot_genes_in_pseudotime | Plots expression for one or more genes as a function of... |
| plot_genes_violin | Plot expression for one or more genes as a violin plot |
| plot_pc_variance_explained | Plots the fraction of variance explained by the each... |
| plot_percent_cells_positive | Plots the number of cells expressing one or more genes above... |
| preprocess_cds | Preprocess a cds to prepare for trajectory inference |
| preprocess_transform | Apply a preprocess transform model to a cell_data_set. |
| principal_graph | Generic to extract principal graph from CDS |
| principal_graph_aux | Generic to extract principal graph auxiliary information from... |
| principal_graph_aux-cell_data_set-method | Method to extract principal graph auxiliary information from... |
| principal_graph_aux-set | Generic to set principal graph auxiliary information into CDS |
| principal_graph_aux-set-cell_data_set-method | Method to set principal graph auxiliary information into CDS |
| principal_graph-cell_data_set-method | Method to extract principal graph from CDS |
| principal_graph-set | Generic to set principal graph to CDS |
| principal_graph-set-cell_data_set-method | Generic to set principal graph to CDS |
| pseudotime | Generic to extract pseudotime from CDS object |
| pseudotime-cell_data_set-method | Method to extract pseudotime from CDS object |
| reduce_dimension | Compute a projection of a cell_data_set object into a lower... |
| reduce_dimension_transform | Apply a reduce_dimension transform model to a cell_data_set. |
| repmat | function to reproduce the behavior of repmat function in... |
| save_monocle_objects | Save a Monocle3 full cell_data_set. |
| save_transform_models | Save cell_data_set transform models. |
| search_cds_nn_index | Search a nearest neighbor index that is stored in the cds. |
| search_nn_index | Search a nearest neighbor index. |
| search_nn_matrix | Search a subject matrix for nearest neighbors to a... |
| set_cds_nn_index | Set a nearest neighor index in the cell_data_set. |
| set_nn_control | Verify and set nearest neighbor parameter list. |
| size_factors | Get the size factors from a cds object. |
| size_factors-set | Set the size factor values in the cell_data_set |
| soft_assignment | Function to calculate the third term in the objective... |
| sparse_prcomp_irlba | Principal Components Analysis |
| top_markers | Identify the genes most specifically expressed in groups of... |
| transfer_cell_labels | Transfer cell column data from a reference to a query... |
