Man pages for scfurl/m3addon
This package adds to the popular "monocle3"
| add_meta_data_cds | Add colData (aka pData) to a cell_data_set |
| backspin | Backspin |
| calcKNNgraph_euclidean | Calculate k Nearest Neighbors from Euclidean distance metric |
| calcKNNgraph_pearson | Calculate k Nearest Neighbors from Pearson distance metric |
| calculate_gene_dispersion | Calculate dispersion genes in a cell_data_set object |
| check_input | check_input helper |
| cluster_LSI | Cluster LSI |
| cluster_PCA | Still working on this function |
| common_features | Finds common features in a list of cds objects |
| density_peak | Cluster cells using Density Peak algorithm |
| detect_genes | Detects genes above minimum threshold. |
| doubletdetection | Doublet Detection |
| doubletFinder_v3 | doubletFinder |
| enrichmentPlot | GSEA and plot |
| estimate_corrected_score | Calculates geneset scores (corrected) |
| estimate_score | Calculates geneset scores using totals |
| extract_data | Extract data using a set of features |
| get_assay | get_assay helper |
| GMT_to_list | Convert a GMT File to a ragged list of genes |
| groupSums | Helper function for summing sparse matrix groups |
| import_scanpy_h5 | Imports a scanpy h5 object |
| iterative_LSI | Iterative LSI |
| load_cellranger_data_h5 | Make monocle3 cell_data_set using cellranger h5 |
| loadSoupX | Load Data for SoupX |
| load_STARsolo_data | Make monocle3 cell_data_set using STARsolo |
| m3addon | m3addon |
| m3addon-package | This package adds to the popular "monocle3" |
| mnnCorrect_cds | Performs mNN batch correction on PCA data from a cds |
| plot_cells_m3addon | Plots the cells along with their trajectories. |
| plot_geneset | Plot geneset scores as cells |
| plot_genes_violin | Plot violin plot of gene expression by group |
| plot_grouped_geneset | Plot geneset scores as summary plot |
| plot_heatmap | Plot heatmap of gene expression by group |
| plot_pseudotime_heatmap | Plots a pseudotime-ordered, row-centered heatmap |
| plot_rho_delta | Plot rho and delta for Density Peak |
| preprocess_cds | Preprocess a cds to prepare for trajectory inference |
| project_data | Project data from one object into the UMAP embedding a single... |
| pseudobulk | Pseudobulk |
| red_dim_plot | Reduced Dimensionality Plot |
| reduce_dimension | Compute a projection of a cell_data_set object into a lower... |
| remove_duplicated_rows | Removes data (collapses) with duplicated names |
| safe_subset | safe_subset helper |
| scrublet_R | Scrublet |
| segment | Segment a Range |
| select_genes | Select genes in a cell_data_set for dimensionality reduction |
| sfc | Produce nice colors (sf color) |
| sparseRowVariances | Helper function for summing sparse matrix groups |
| split_plot | Plot a fixed size for plot and legend |
| spRing | spRing Execute the spRing algorithm |
| ssgsea | ssGSEA |
| tf_idf_transform | Performs TF-IDF transformation on a cell_data_set |
| tf_idf_transform_v2 | Performs TF-IDF transformation on a cell_data_set v2 |
| trimap | Dimensionality Reduction Using Triplet Constraints |
