NAMESPACE

# Generated by roxygen2: do not edit by hand

S3method(print,VISTA)
export(as_deseq_dataset)
export(as_vista)
export(benchmark_vista_equivalence)
export(comparisons)
export(create_vista)
export(cutoffs)
export(deg_summary)
export(derive_vista_metadata)
export(enrichMsigDB)
export(example_vista)
export(export_vista_assets)
export(get_cell_fractions)
export(get_celltype_barplot)
export(get_celltype_group_dotplot)
export(get_celltype_heatmap)
export(get_corr_heatmap)
export(get_deg_alluvial)
export(get_deg_count_barplot)
export(get_deg_count_donutplot)
export(get_deg_count_pieplot)
export(get_deg_venn_diagram)
export(get_enrichment_chord)
export(get_enrichment_plot)
export(get_expression_barplot)
export(get_expression_boxplot)
export(get_expression_chromosome_plot)
export(get_expression_density)
export(get_expression_heatmap)
export(get_expression_joyplot)
export(get_expression_lineplot)
export(get_expression_lollipop)
export(get_expression_matrix)
export(get_expression_raincloud)
export(get_expression_scatter)
export(get_expression_violinplot)
export(get_foldchange_barplot)
export(get_foldchange_boxplot)
export(get_foldchange_chromosome_plot)
export(get_foldchange_heatmap)
export(get_foldchange_lineplot)
export(get_foldchange_lollipop)
export(get_foldchange_matrix)
export(get_foldchange_raincloud)
export(get_foldchange_scatter)
export(get_genes_by_regulation)
export(get_go_enrichment)
export(get_gsea)
export(get_kegg_enrichment)
export(get_ma_plot)
export(get_mds_plot)
export(get_msigdb_enrichment)
export(get_pairwise_corr_plot)
export(get_pathway_genes)
export(get_pathway_heatmap)
export(get_pca_plot)
export(get_umap_plot)
export(get_volcano_plot)
export(group_colors)
export(group_palette)
export(match_vista_inputs)
export(norm_counts)
export(read_vista_counts)
export(read_vista_metadata)
export(row_data)
export(run_cell_deconvolution)
export(run_deseq_analysis)
export(run_edger_analysis)
export(run_limma_analysis)
export(run_vista_report)
export(sample_info)
export(save_vista_data)
export(save_vista_plot)
export(set_de_source)
export(set_rowdata)
export(set_vista_comparison_colors)
export(set_vista_group_colors)
export(validate_vista)
export(validate_vista_deep)
exportClasses(VISTA)
exportMethods("[")
exportMethods(comparisons)
exportMethods(counts)
exportMethods(cutoffs)
exportMethods(deg_summary)
exportMethods(group_colors)
exportMethods(group_palette)
exportMethods(norm_counts)
exportMethods(row_data)
exportMethods(sample_info)
exportMethods(show)
exportMethods(updateObject)
importClassesFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(AnnotationDbi,keys)
importFrom(AnnotationDbi,mapIds)
importFrom(BiocGenerics,counts)
importFrom(BiocGenerics,updateObject)
importFrom(DESeq2,DESeq)
importFrom(DESeq2,DESeqDataSetFromMatrix)
importFrom(DESeq2,counts)
importFrom(DESeq2,estimateSizeFactors)
importFrom(DESeq2,results)
importFrom(GGally,ggpairs)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,metadata)
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(cli,cli_abort)
importFrom(cli,cli_inform)
importFrom(cli,cli_warn)
importFrom(clusterProfiler,GSEA)
importFrom(clusterProfiler,enrichGO)
importFrom(clusterProfiler,enrichKEGG)
importFrom(clusterProfiler,enricher)
importFrom(clusterProfiler,gseGO)
importFrom(clusterProfiler,gseKEGG)
importFrom(colorspace,qualitative_hcl)
importFrom(dplyr,"%>%")
importFrom(dplyr,arrange)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,pull)
importFrom(dplyr,select)
importFrom(dplyr,summarise)
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(edgeR,estimateDisp)
importFrom(edgeR,glmQLFTest)
importFrom(edgeR,glmQLFit)
importFrom(edgeR,topTags)
importFrom(ggplot2,aes)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_density)
importFrom(ggplot2,geom_jitter)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,labs)
importFrom(ggplot2,position_jitter)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_discrete)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_minimal)
importFrom(ggpubr,ggbarplot)
importFrom(ggpubr,stat_compare_means)
importFrom(methods,callNextMethod)
importFrom(methods,setClass)
importFrom(methods,setGeneric)
importFrom(methods,setMethod)
importFrom(methods,setValidity)
importFrom(methods,show)
importFrom(msigdbr,msigdbr)
importFrom(rlang,.data)
importFrom(rlang,`%||%`)
importFrom(rlang,abort)
importFrom(stats,as.dist)
importFrom(stats,cmdscale)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,na.omit)
importFrom(stats,prcomp)
importFrom(stats,setNames)
importFrom(stringr,str_c)
importFrom(stringr,str_detect)
importFrom(stringr,str_replace)
importFrom(tibble,as_tibble)
importFrom(tibble,column_to_rownames)
importFrom(tibble,rownames_to_column)
importFrom(tibble,tibble)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,pivot_wider)
importFrom(utils,getFromNamespace)
importFrom(utils,head)