| add_densmap | run densMAP and store the result in reducedDim(x, "DENSMAP") |
| add_plate_metrics | some metrics than have come in handy for plate-seq... |
| add_static_trace | Refactoring plot_velo into multiple functions moving forwards |
| add_tpm | partition transcripts per million between spliced and... |
| add_umap_embedding | run UMAP with 'uwot' and store the embedding model in... |
| add_velo_trace | Refactoring plot_velo into multiple functions moving forwards |
| adt_seqs_from_hdf5 | dump ADT/HTO sequences from an h5 mRNA+ADT file for... |
| adts_from_hdf5 | grab ADT/HTO matrices from an h5 mRNA+ADT file |
| biotypes | Get or set rowData(object), biotype columns in a... |
| cellrank | Cell trajectories with 'CellRank' |
| check_sce | check that an SCE will be suitable for muscat, scvelo,... |
| cluster_velo_txis | Simple Louvain, density, or k-means clustering. Doesn't use... |
| compute_velocity | velocity wrapper, modularizes pipelined loading |
| dedupe_velo_txis | deduplicate symbols in a SingleCellExperiment object with... |
| diff_AB | this is kind of a helper function, but useful enough to split... |
| downsample_txis | blockwise downsampling: try to preserve balanced clusters... |
| fetch_ensembl | convenience function for fetching ENSEMBL annotations (genes... |
| find_doublets | simple automated doublet marking for pipelining, refactored a... |
| find_dupe_txis | Mark duplicated mcols(txis)$symbol in a SingleCellExperiment... |
| find_eligible_cells | Find cells that meet certain cluster-wise criteria |
| fit_mixtures | Fit mixtures. Turns out this was useful outside of... |
| fix_cells | fix or drop cells with an size factor of 0 (which will crash... |
| fix_gencode | helper function to make Gencode version decoding slightly... |
| fix_rownames | strip silly ENSEMBL gene/transcript version IDs |
| get_AB | a shim function, mostly to feed plot_ABC() |
| get_ensembl_genes | Simple wrapper to annotate genes/transcripts with symbols and... |
| get_ensembl_transcripts | Get transcripts grouped by gene name. |
| get_gencode_ensembl | Gencode releases do not map 1:1 onto ENSEMBL releases, hence... |
| get_gencode_genes | A wrapper for get_ensembl_genes, to handle Gencode release... |
| get_gencode_species | Gencode prefaces mouse releases with an M, and human releases... |
| get_gencode_transcripts | Just like get_ensembl_transcripts, but for gencode. |
| get_sample_from_barcode | Extract the sample/batch name for each cell from a... |
| harmonize_velo_txis | harness for velocity correction (currently ignorant of... |
| import_droplet_txis | import droplet RNAseq data (usually from Alevin) into a... |
| import_kallisto_txis | import plate-seq runs from Kallisto into a... |
| import_plate_txis | import plate-seq velocity information (from Salmon) to a... |
| import_velo_txis | import velocity information (usually from Alevin) into a... |
| infercnv | massage a (possibly velocitized) SingleCellExperiment into an... |
| izar_transform | generalizes the transformation from Izar et al 2020 for... |
| label_cells | barebones cell labeling function |
| load_mtx | Load a triple of gene names, cell names, gene x cell counts... |
| make_plate_plot | plot outcomes of 96-, 384-, or 1536-well plate sequencing... |
| make_storm_trimmer | simple function to emit a trimming script for STORM-seq preps |
| make_tximeta | downstream processor for make_spliced_index results... |
| make_velo_index | aped from... |
| merge_sces | convenience function for merging datasets after QC (e.g.... |
| nonzero | find nonzero entries in a sparse (dgcMatrix) matrix |
| plot_ABC | plot compartments from samples A & B, perhaps by diffing... |
| plot_densities | another helper that grew into a real live function (albeit a... |
| plot_eligible_cells | Plot a heatmap of cells x samples that fit certain sampling... |
| plot_features | some equivalents to Seurat standards, with or without... |
| plot_velo | Generate interactive 3D UMAP plot with cones for velocity.... |
| process_velo_txis | Load some Alevin runs quantified with velocity information |
| project_onto_umap | given a 'uwot' model in metadata(x)$uwot, project y onto... |
| relevel_sequentially | convenience function for reordering factors without thinking... |
| rescale_dimred | rescale a reduced-dimensional representation for plotting... |
| sample_clusters | simple downsampling for NMF/NTF exploratory work and big... |
| scdb | automates fetching of Valentine Svenssen's single-cell... |
| split_SE | convenience function: split a Summarized/SingleCellExperiment... |
| veload | world's dumbest velocity loader, currently only for Alevin... |
| velocity_assays | Get or set assays particular to velocitized... |
| velocity_metadata | Get or set metadata items for velocitized... |
