NAMESPACE

# Generated by roxygen2: do not edit by hand

export("embedded<-")
export("gene_biotype<-")
export("scVelo<-")
export("spliced<-")
export("transcript_biotype<-")
export("unspliced<-")
export(add_densmap)
export(add_plate_metrics)
export(add_tpm)
export(add_umap_embedding)
export(adt_seqs_from_hdf5)
export(adts_from_hdf5)
export(cellrank)
export(check_sce)
export(cluster_velo_txis)
export(compute_velocity)
export(dedupe_velo_txis)
export(diff_AB)
export(downsample_txis)
export(drop_doublets)
export(embedded)
export(fetch_ensembl)
export(find_doublets)
export(find_dupe_txis)
export(find_eligible_cells)
export(fit_mixtures)
export(fix_cells)
export(fix_gencode)
export(fix_rownames)
export(gene_biotype)
export(get_AB)
export(get_ensembl_genes)
export(get_ensembl_transcripts)
export(get_gencode_ensembl)
export(get_gencode_genes)
export(get_gencode_species)
export(get_gencode_transcripts)
export(get_sample_from_barcode)
export(harmonize_velo_txis)
export(import_droplet_txis)
export(import_kallisto_txis)
export(import_plate_txis)
export(import_velo_txis)
export(infercnv)
export(izar_transform)
export(label_cells)
export(load_mtx)
export(make_plate_plot)
export(make_storm_trimmer)
export(make_tximeta)
export(make_velo_index)
export(merge_sces)
export(nonzero)
export(nz)
export(nz_bycol)
export(nz_byrow)
export(nz_colnames)
export(nz_cols)
export(nz_rownames)
export(nz_rows)
export(plot_ABC)
export(plot_densities)
export(plot_eligible_cells)
export(plot_features)
export(plot_velo)
export(process_velo_txis)
export(project_onto_umap)
export(relevel_sequentially)
export(res)
export(rescale_dimred)
export(sample_clusters)
export(scVelo)
export(scdb)
export(spliced)
export(split_SE)
export(transcript_biotype)
export(unspliced)
export(veload)
exportMethods("embedded<-")
exportMethods("gene_biotype<-")
exportMethods("scVelo<-")
exportMethods("spliced<-")
exportMethods("transcript_biotype<-")
exportMethods("unspliced<-")
exportMethods(cellrank)
exportMethods(embedded)
exportMethods(gene_biotype)
exportMethods(scVelo)
exportMethods(spliced)
exportMethods(transcript_biotype)
exportMethods(unspliced)
import(AnnotationHub)
import(BiocGenerics)
import(BiocParallel)
import(Biostrings)
import(GenomeInfoDb)
import(GenomicFeatures)
import(GenomicRanges)
import(HDF5Array)
import(Matrix)
import(MatrixGenerics)
import(Polychrome)
import(SingleCellExperiment)
import(SingleR)
import(SummarizedExperiment)
import(basilisk)
import(compartmap)
import(densvis)
import(eisaR)
import(fishpond)
import(jsonlite)
import(mbkmeans)
import(mclust)
import(platetools)
import(plotly)
import(rhdf5)
import(rtracklayer)
import(scDblFinder)
import(scater)
import(scran)
import(scuttle)
import(tximeta)
import(tximport)
import(uwot)
import(velociraptor)
import(viridis)
import(viridisLite)
importFrom(BiocGenerics,sizeFactors)
importFrom(ComplexHeatmap,Heatmap)
importFrom(DelayedArray,is_sparse)
importFrom(DelayedArray,t)
importFrom(Matrix,t)
importFrom(Nebulosa,plot_density)
importFrom(S4Vectors,DataFrame)
importFrom(SingleCellExperiment,reducedDim)
importFrom(SingleCellExperiment,reducedDimNames)
importFrom(basilisk,BasiliskEnvironment)
importFrom(densityClust,densityClust)
importFrom(densityClust,findClusters)
importFrom(ensembldb,genes)
importFrom(ensembldb,transcripts)
importFrom(ensembldb,transcriptsBy)
importFrom(igraph,cluster_louvain)
importFrom(reticulate,import)
importFrom(scran,buildSNNGraph)
importFrom(scuttle,cleanSizeFactors)
importFrom(scuttle,librarySizeFactors)
importFrom(scuttle,normalizeCounts)
importFrom(utils,read.delim)
importFrom(zellkonverter,.AnnDataDependencies)
importFrom(zellkonverter,AnnData2SCE)