# Generated by roxygen2: do not edit by hand

S3method(clustify,Seurat)
S3method(clustify,SingleCellExperiment)
S3method(clustify,default)
S3method(clustify,seurat)
S3method(clustify_lists,Seurat)
S3method(clustify_lists,SingleCellExperiment)
S3method(clustify_lists,default)
S3method(clustify_lists,seurat)
S3method(clustify_nudge,Seurat)
S3method(clustify_nudge,default)
S3method(clustify_nudge,seurat)
S3method(object_data,Seurat)
S3method(object_data,SingleCellExperiment)
S3method(object_data,seurat)
S3method(object_ref,Seurat)
S3method(object_ref,SingleCellExperiment)
S3method(object_ref,default)
S3method(object_ref,seurat)
S3method(seurat_meta,Seurat)
S3method(seurat_meta,seurat)
S3method(seurat_ref,Seurat)
S3method(seurat_ref,seurat)
S3method(write_meta,Seurat)
S3method(write_meta,SingleCellExperiment)
S3method(write_meta,seurat)
export(average_clusters)
export(binarize_expr)
export(calculate_pathway_gsea)
export(call_consensus)
export(call_to_metadata)
export(clustify)
export(clustify_lists)
export(clustify_nudge)
export(clustifyr_methods)
export(collapse_to_cluster)
export(compare_lists)
export(cor_to_call)
export(cor_to_call_rank)
export(cor_to_call_topn)
export(downsample_matrix)
export(feature_select_PCA)
export(file_marker_parse)
export(find_rank_bias)
export(gene_pct_markerm)
export(get_vargenes)
export(gmt_to_list)
export(insert_meta_object)
export(marker_select)
export(matrixize_markers)
export(object_data)
export(object_ref)
export(overcluster)
export(overcluster_test)
export(parse_loc_object)
export(plot_best_call)
export(plot_cor)
export(plot_cor_heatmap)
export(plot_dims)
export(plot_gene)
export(plot_pathway_gsea)
export(pos_neg_marker)
export(pos_neg_select)
export(ref_feature_select)
export(ref_marker_select)
export(reverse_marker_matrix)
export(run_gsea)
export(seurat_meta)
export(seurat_ref)
export(write_meta)
import(Matrix)
import(dplyr)
import(entropy)
import(ggplot2)
import(scales)
import(tibble)
importFrom(S4Vectors,DataFrame)
importFrom(SingleCellExperiment,colData)
importFrom(SingleCellExperiment,logcounts)
importFrom(SummarizedExperiment,`colData<-`)
importFrom(cowplot,theme_cowplot)
importFrom(fgsea,fgsea)
importFrom(matrixStats,colRanks)
importFrom(matrixStats,rowMaxs)
importFrom(matrixStats,rowMedians)
importFrom(methods,is)
importFrom(rlang,":=")
importFrom(stats,cor)
importFrom(stats,dhyper)
importFrom(stats,median)
importFrom(stats,p.adjust)
importFrom(stats,prcomp)
importFrom(stats,quantile)
importFrom(tidyr,gather)
