NAMESPACE

# Generated by roxygen2: do not edit by hand

export(.calculate_retain_parameter)
export(.doublet_finder_plot_dim_red)
export(.doublet_finder_plot_param_sweep)
export(.perform_ks_uniformity_test)
export(.plot_emptydrops_distribution)
export(.plot_emptydrops_loglike)
export(annotate_celltype_metrics)
export(annotate_integrated_sce)
export(annotate_merged_sce)
export(annotate_sce)
export(annotate_sce_cells)
export(annotate_sce_genes)
export(cluster_sce)
export(filter_sce)
export(find_cells)
export(find_impacted_pathways)
export(find_marker_genes)
export(find_singlets)
export(generate_sce)
export(integrate_sce)
export(liger_preprocess)
export(liger_reduce_dims)
export(list_databases)
export(map_celltypes_sce)
export(map_custom_celltypes)
export(map_ensembl_gene_id)
export(merge_sce)
export(model_celltype_freqs)
export(pathway_analysis_enrichr)
export(pathway_analysis_webgestaltr)
export(perform_de)
export(plot_expr_by_numeric_var)
export(plot_reduced_dim)
export(plot_reduced_dim_gene)
export(plot_violin)
export(pseudobulk_sce)
export(read_celltype_mappings)
export(read_metadata)
export(read_sce)
export(read_sparse_matrix)
export(reduce_dims_sce)
export(report_celltype_metrics)
export(report_celltype_model)
export(report_de)
export(report_impacted_pathway)
export(report_integrated_sce)
export(report_merged_sce)
export(report_qc_sce)
export(volcano_plot)
export(write_celltype_mappings)
export(write_sce)
export(write_sparse_matrix)
import(Seurat)
import(SingleCellExperiment, except = "cpm")
import(cli)
import(ggplot2)
import(scater, except = "normalize")
importFrom(DirichletReg,DR_data)
importFrom(DirichletReg,DirichReg)
importFrom(DoubletFinder,doubletFinder)
importFrom(DoubletFinder,find.pK)
importFrom(DoubletFinder,modelHomotypic)
importFrom(DoubletFinder,paramSweep)
importFrom(DoubletFinder,summarizeSweep)
importFrom(DropletUtils,barcodeRanks)
importFrom(DropletUtils,emptyDrops)
importFrom(EWCE,bootstrap_enrichment_test)
importFrom(EWCE,generate_celltype_data)
importFrom(MAST,SceToSingleCellAssay)
importFrom(MAST,summary)
importFrom(MAST,zlm)
importFrom(Matrix,Matrix)
importFrom(Matrix,colSums)
importFrom(Matrix,rowSums)
importFrom(Matrix,t)
importFrom(Matrix,writeMM)
importFrom(R.utils,gzip)
importFrom(Rtsne,Rtsne)
importFrom(Seurat,CreateSeuratObject)
importFrom(Seurat,FindVariableFeatures)
importFrom(Seurat,NormalizeData)
importFrom(Seurat,RunPCA)
importFrom(Seurat,RunTSNE)
importFrom(Seurat,RunUMAP)
importFrom(Seurat,SCTransform)
importFrom(Seurat,ScaleData)
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(SingleCellExperiment,counts)
importFrom(SingleCellExperiment,logcounts)
importFrom(SingleCellExperiment,normcounts)
importFrom(SingleCellExperiment,reducedDim)
importFrom(SingleCellExperiment,reducedDimNames)
importFrom(SingleCellExperiment,reducedDims)
importFrom(SingleCellExperiment,tpm)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(UpSetR,fromList)
importFrom(UpSetR,upset)
importFrom(WebGestaltR,WebGestaltR)
importFrom(WebGestaltR,listGeneSet)
importFrom(assertthat,are_equal)
importFrom(assertthat,assert_that)
importFrom(assertthat,is.scalar)
importFrom(bib2df,bib2df)
importFrom(biomaRt,getBM)
importFrom(biomaRt,useEnsembl)
importFrom(cli,cli_alert)
importFrom(cli,cli_alert_danger)
importFrom(cli,cli_alert_info)
importFrom(cli,cli_alert_success)
importFrom(cli,cli_alert_warning)
importFrom(cli,cli_h1)
importFrom(cli,cli_h2)
importFrom(cli,cli_h3)
importFrom(cli,cli_text)
importFrom(cli,cli_ul)
importFrom(cli,col_green)
importFrom(cli,rule)
importFrom(cli,symbol)
importFrom(cowplot,background_grid)
importFrom(cowplot,theme_cowplot)
importFrom(dplyr,"%>%")
importFrom(dplyr,arrange)
importFrom(dplyr,case_when)
importFrom(dplyr,count)
importFrom(dplyr,dense_rank)
importFrom(dplyr,desc)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,inner_join)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,mutate_if)
importFrom(dplyr,n)
importFrom(dplyr,pull)
importFrom(dplyr,rename)
importFrom(dplyr,rename_all)
importFrom(dplyr,select)
importFrom(dplyr,slice_head)
importFrom(dplyr,summarise_each)
importFrom(dplyr,summarize)
importFrom(dplyr,tally)
importFrom(dplyr,top_n)
importFrom(dplyr,ungroup)
importFrom(dplyr,union)
importFrom(edgeR,cpm)
importFrom(english,words)
importFrom(enrichR,enrichr)
importFrom(enrichR,listEnrichrDbs)
importFrom(forcats,fct_reorder)
importFrom(formattable,formattable)
importFrom(formattable,icontext)
importFrom(future,availableCores)
importFrom(future.apply,future_lapply)
importFrom(ggdendro,ggdendrogram)
importFrom(ggplot2,aes)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggplotGrob)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme_bw)
importFrom(ggpubr,as_ggplot)
importFrom(ggpubr,ggarrange)
importFrom(ggrepel,geom_text_repel)
importFrom(ggridges,geom_density_ridges_gradient)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,nclass.Sturges)
importFrom(grDevices,rgb)
importFrom(kBET,kBET)
importFrom(leaflet,colorFactor)
importFrom(limma,is.fullrank)
importFrom(limma,nonEstimable)
importFrom(limma,normalizeQuantiles)
importFrom(magrittr,"%>%")
importFrom(magrittr,set_colnames)
importFrom(methods,as)
importFrom(monocle3,cluster_cells)
importFrom(monocle3,new_cell_data_set)
importFrom(monocle3,plot_genes_by_group)
importFrom(monocle3,preprocess_cds)
importFrom(monocle3,top_markers)
importFrom(paletteer,paletteer_d)
importFrom(parallel,mclapply)
importFrom(patchwork,plot_layout)
importFrom(plotly,plot_ly)
importFrom(plyr,adply)
importFrom(preprocessCore,normalize.quantiles)
importFrom(purrr,discard)
importFrom(purrr,map)
importFrom(purrr,map_chr)
importFrom(purrr,map_df)
importFrom(purrr,map_if)
importFrom(purrr,map_int)
importFrom(purrr,map_lgl)
importFrom(purrr,pmap)
importFrom(purrr,set_names)
importFrom(purrr,walk)
importFrom(qs,qread)
importFrom(qs,qsave)
importFrom(rliger,createLiger)
importFrom(rliger,normalize)
importFrom(rliger,optimizeALS)
importFrom(rliger,quantile_norm)
importFrom(rliger,removeMissingObs)
importFrom(rliger,scaleNotCenter)
importFrom(rliger,selectGenes)
importFrom(rmarkdown,render)
importFrom(scales,percent)
importFrom(scales,percent_format)
importFrom(scales,pretty_breaks)
importFrom(sctransform,correct_counts)
importFrom(sctransform,get_residual_var)
importFrom(sctransform,get_residuals)
importFrom(sctransform,vst)
importFrom(stats,as.formula)
importFrom(stats,coef)
importFrom(stats,dist)
importFrom(stats,fisher.test)
importFrom(stats,hclust)
importFrom(stats,lm)
importFrom(stats,mad)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,predict)
importFrom(stats,quantile)
importFrom(stats,relevel)
importFrom(stats,reorder)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stringr,str_replace)
importFrom(stringr,str_split)
importFrom(stringr,str_wrap)
importFrom(threejs,scatterplot3js)
importFrom(tibble,rownames_to_column)
importFrom(tibble,tibble)
importFrom(tidyr,drop_na)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,pivot_wider)
importFrom(tidyselect,all_of)
importFrom(tools,file_path_sans_ext)
importFrom(tools,toTitleCase)
importFrom(utils,read.csv)
importFrom(utils,read.delim)
importFrom(utils,read.table)
importFrom(utils,write.table)
importFrom(uwot,umap)