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NAMESPACE
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# Generated by roxygen2: do not edit by hand
S3method(annotate_cell_type,HPCell)
S3method(calculate_pseudobulk,HPCell)
S3method(evaluate_hpc,HPCell)
S3method(get_single_cell,HPCell)
S3method(normalise_abundance_seurat_SCT,HPCell)
S3method(print,HPCell)
S3method(remove_dead_scuttle,HPCell)
S3method(remove_doublets_scDblFinder,HPCell)
S3method(remove_empty_DropletUtils,HPCell)
S3method(remove_empty_DropletUtils,Seurat)
S3method(remove_empty_threshold,HPCell)
S3method(remove_empty_threshold,Seurat)
S3method(score_cell_cycle_seurat,HPCell)
S3method(transform_assay,HPCell)
export(alive_identification)
export(annotate_cell_type)
export(annotation_label_transfer)
export(calculate_pseudobulk)
export(cell_cycle_scoring)
export(clean_cellxgene_cell_types)
export(compute_mode_delayedarray)
export(convert_gene_names)
export(create_pseudobulk)
export(delete_lines_with_word)
export(doublet_identification)
export(empty_droplet_id)
export(empty_droplet_threshold)
export(evaluate_hpc)
export(factory_de_fix_effect)
export(factory_de_random_effect)
export(feature_chunks)
export(find_variable_genes)
export(get_positions)
export(get_single_cell)
export(get_unique_tissues)
export(hpc_internal)
export(hpc_internal_report)
export(hpc_iterate)
export(hpc_merge)
export(hpc_report)
export(hpc_single)
export(initialise_hpc)
export(internal_de_function)
export(is_target)
export(map2_test_differential_abundance_hpc)
export(map_add_dispersion_to_se)
export(map_de)
export(map_split_sce_by_gene)
export(map_split_se_by_gene)
export(map_split_se_by_number_of_genes)
export(map_test_differential_abundance)
export(non_batch_variation_removal)
export(normalise_abundance_seurat_SCT)
export(preprocessing_output)
export(pseudobulk_merge)
export(read_data_container)
export(reference_annotation_to_consensus)
export(reference_label_coarse_id)
export(reference_label_fine_id)
export(remove_dead_scuttle)
export(remove_doublets_scDblFinder)
export(remove_empty_DropletUtils)
export(remove_empty_threshold)
export(save_experiment_data)
export(score_cell_cycle_seurat)
export(se_add_dispersion)
export(split_summarized_experiment)
export(target_append)
export(test_differential_abundance_hpc)
export(transform_assay)
export(transform_utility)
export(vector_to_code)
exportMethods(test_differential_abundance)
import(DelayedArray)
import(Seurat)
import(SeuratObject)
import(SingleCellExperiment)
import(broom)
import(crew)
import(crew.cluster)
import(dplyr)
import(ggplot2)
import(ggupset)
import(here)
import(qs)
import(scDblFinder)
import(tarchetypes)
import(targets)
import(tidySingleCellExperiment)
import(tidySummarizedExperiment)
import(tidyseurat)
importFrom(AnnotationDbi,mapIds)
importFrom(Azimuth,RunAzimuth)
importFrom(DelayedArray,blockApply)
importFrom(DropletUtils,barcodeRanks)
importFrom(DropletUtils,emptyDrops)
importFrom(EnsDb.Hsapiens.v86,EnsDb.Hsapiens.v86)
importFrom(HDF5Array,loadHDF5SummarizedExperiment)
importFrom(HDF5Array,saveHDF5SummarizedExperiment)
importFrom(Matrix,Matrix)
importFrom(Matrix,colSums)
importFrom(S4Vectors,cbind)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,split)
importFrom(Seurat,Assays)
importFrom(Seurat,CellCycleScoring)
importFrom(Seurat,CreateAssayObject)
importFrom(Seurat,CreateSeuratObject)
importFrom(Seurat,DefaultAssay)
importFrom(Seurat,FindClusters)
importFrom(Seurat,FindNeighbors)
importFrom(Seurat,FindTransferAnchors)
importFrom(Seurat,FindVariableFeatures)
importFrom(Seurat,GetAssayData)
importFrom(Seurat,MapQuery)
importFrom(Seurat,NormalizeData)
importFrom(Seurat,PercentageFeatureSet)
importFrom(Seurat,RunPCA)
importFrom(Seurat,RunUMAP)
importFrom(Seurat,SCTransform)
importFrom(Seurat,ScaleData)
importFrom(Seurat,VariableFeatures)
importFrom(Seurat,as.Seurat)
importFrom(Seurat,as.SingleCellExperiment)
importFrom(SeuratObject,RenameAssays)
importFrom(SingleCellExperiment,"altExp<-")
importFrom(SingleCellExperiment,"reducedDim<-")
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(SingleCellExperiment,altExp)
importFrom(SingleR,SingleR)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"assays<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(biomaRt,getBM)
importFrom(biomaRt,useMart)
importFrom(callr,r)
importFrom(celldex,BlueprintEncodeData)
importFrom(celldex,MonacoImmuneData)
importFrom(crew,crew_controller_local)
importFrom(data.table,":=")
importFrom(digest,digest)
importFrom(dplyr,as_tibble)
importFrom(dplyr,case_when)
importFrom(dplyr,count)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,join_by)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,pull)
importFrom(dplyr,quo_name)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,summarise)
importFrom(dplyr,tibble)
importFrom(dplyr,tribble)
importFrom(dplyr,with_groups)
importFrom(edgeR,estimateDisp)
importFrom(future,tweak)
importFrom(glue,glue)
importFrom(here,here)
importFrom(ids,random_id)
importFrom(lme4,findbars)
importFrom(magrittr,"%$%")
importFrom(magrittr,"%>%")
importFrom(magrittr,divide_by)
importFrom(magrittr,extract2)
importFrom(magrittr,not)
importFrom(magrittr,set_names)
importFrom(methods,as)
importFrom(methods,show)
importFrom(purrr,compact)
importFrom(purrr,imap)
importFrom(purrr,map)
importFrom(purrr,map2)
importFrom(purrr,map_chr)
importFrom(purrr,map_int)
importFrom(purrr,safely)
importFrom(purrr,set_names)
importFrom(readr,write_lines)
importFrom(rlang,enquo)
importFrom(rlang,is_symbolic)
importFrom(rlang,parse_expr)
importFrom(rlang,quo_is_symbolic)
importFrom(rlang,rep_along)
importFrom(rlang,sym)
importFrom(scater,isOutlier)
importFrom(scuttle,logNormCounts)
importFrom(scuttle,perCellQCMetrics)
importFrom(stats,as.formula)
importFrom(stats,density)
importFrom(stats,model.matrix)
importFrom(stats,terms)
importFrom(stats,update)
importFrom(stringr,str_c)
importFrom(stringr,str_detect)
importFrom(stringr,str_remove)
importFrom(stringr,str_remove_all)
importFrom(stringr,str_replace)
importFrom(stringr,str_replace_all)
importFrom(stringr,str_subset)
importFrom(stringr,str_trim)
importFrom(stringr,str_which)
importFrom(targets,tar_config_get)
importFrom(targets,tar_option_set)
importFrom(targets,tar_script)
importFrom(tibble,as_tibble)
importFrom(tibble,deframe)
importFrom(tibble,enframe)
importFrom(tibble,rowid_to_column)
importFrom(tibble,rownames_to_column)
importFrom(tibble,tibble)
importFrom(tidybulk,as_SummarizedExperiment)
importFrom(tidybulk,pivot_transcript)
importFrom(tidybulk,test_differential_abundance)
importFrom(tidyr,expand_grid)
importFrom(tidyr,nest)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,replace_na)
importFrom(tidyr,unite)
importFrom(tidyr,unnest)
importFrom(tidyselect,all_of)
importFrom(tidyseurat,aggregate_cells)
importFrom(utils,capture.output)
importMethodsFrom(ensembldb,genes)