Man pages for trichelab/velocessor
The world's dumbest single-cell RNA velocity calculator and loader

add_densmaprun densMAP and store the result in reducedDim(x, "DENSMAP")
add_plate_metricssome metrics than have come in handy for plate-seq...
add_static_traceRefactoring plot_velo into multiple functions moving forwards
add_tpmpartition transcripts per million between spliced and...
add_umap_embeddingrun UMAP with 'uwot' and store the embedding model in...
add_velo_traceRefactoring plot_velo into multiple functions moving forwards
adt_seqs_from_hdf5dump ADT/HTO sequences from an h5 mRNA+ADT file for...
adts_from_hdf5grab ADT/HTO matrices from an h5 mRNA+ADT file
biotypesGet or set rowData(object), biotype columns in a...
cellrankCell trajectories with 'CellRank'
check_scecheck that an SCE will be suitable for muscat, scvelo,...
cluster_velo_txisSimple Louvain, density, or k-means clustering. Doesn't use...
compute_velocityvelocity wrapper, modularizes pipelined loading
dedupe_velo_txisdeduplicate symbols in a SingleCellExperiment object with...
diff_ABthis is kind of a helper function, but useful enough to split...
downsample_txisblockwise downsampling: try to preserve balanced clusters...
fetch_ensemblconvenience function for fetching ENSEMBL annotations (genes...
find_doubletssimple automated doublet marking for pipelining, refactored a...
find_dupe_txisMark duplicated mcols(txis)$symbol in a SingleCellExperiment...
find_eligible_cellsFind cells that meet certain cluster-wise criteria
fit_mixturesFit mixtures. Turns out this was useful outside of...
fix_cellsfix or drop cells with an size factor of 0 (which will crash...
fix_gencodehelper function to make Gencode version decoding slightly...
fix_rownamesstrip silly ENSEMBL gene/transcript version IDs
get_ABa shim function, mostly to feed plot_ABC()
get_ensembl_genesSimple wrapper to annotate genes/transcripts with symbols and...
get_ensembl_transcriptsGet transcripts grouped by gene name.
get_gencode_ensemblGencode releases do not map 1:1 onto ENSEMBL releases, hence...
get_gencode_genesA wrapper for get_ensembl_genes, to handle Gencode release...
get_gencode_speciesGencode prefaces mouse releases with an M, and human releases...
get_gencode_transcriptsJust like get_ensembl_transcripts, but for gencode.
get_sample_from_barcodeExtract the sample/batch name for each cell from a...
harmonize_velo_txisharness for velocity correction (currently ignorant of...
import_droplet_txisimport droplet RNAseq data (usually from Alevin) into a...
import_kallisto_txisimport plate-seq runs from Kallisto into a...
import_plate_txisimport plate-seq velocity information (from Salmon) to a...
import_velo_txisimport velocity information (usually from Alevin) into a...
infercnvmassage a (possibly velocitized) SingleCellExperiment into an...
izar_transformgeneralizes the transformation from Izar et al 2020 for...
label_cellsbarebones cell labeling function
load_mtxLoad a triple of gene names, cell names, gene x cell counts...
make_plate_plotplot outcomes of 96-, 384-, or 1536-well plate sequencing...
make_storm_trimmersimple function to emit a trimming script for STORM-seq preps
make_tximetadownstream processor for make_spliced_index results...
make_velo_indexaped from...
merge_scesconvenience function for merging datasets after QC (e.g....
nonzerofind nonzero entries in a sparse (dgcMatrix) matrix
plot_ABCplot compartments from samples A & B, perhaps by diffing...
plot_densitiesanother helper that grew into a real live function (albeit a...
plot_eligible_cellsPlot a heatmap of cells x samples that fit certain sampling...
plot_featuressome equivalents to Seurat standards, with or without...
plot_veloGenerate interactive 3D UMAP plot with cones for velocity....
process_velo_txisLoad some Alevin runs quantified with velocity information
project_onto_umapgiven a 'uwot' model in metadata(x)$uwot, project y onto...
relevel_sequentiallyconvenience function for reordering factors without thinking...
rescale_dimredrescale a reduced-dimensional representation for plotting...
sample_clusterssimple downsampling for NMF/NTF exploratory work and big...
scdbautomates fetching of Valentine Svenssen's single-cell...
split_SEconvenience function: split a Summarized/SingleCellExperiment...
veloadworld's dumbest velocity loader, currently only for Alevin...
velocity_assaysGet or set assays particular to velocitized...
velocity_metadataGet or set metadata items for velocitized...
trichelab/velocessor documentation built on Jan. 5, 2022, 6:27 p.m.