NAMESPACE

# Generated by roxygen2: do not edit by hand

export(CountTableFromFeatureCounts)
export(ReadFeatureCounts)
export(add_missing_rows)
export(align_signature)
export(assay)
export(calculate_correlations)
export(colData)
export(compare_one_to_many)
export(correlation_matrix)
export(deseq_analysis)
export(detect_wbc)
export(drop_na_cols)
export(drop_na_rows)
export(filter_edgeR)
export(filtered_hazard_ratio_table)
export(gene_wilcox_test)
export(getGenes)
export(get_events_breakdown)
export(get_fc_list)
export(gsea_analysis)
export(hazard_ratios_table)
export(hclust_estimator)
export(install_packages_from_script)
export(kmeans_estimator)
export(log_rank_test)
export(make_composite_coding)
export(make_phenotypes)
export(make_se)
export(nmf_estimator)
export(nmf_plotter)
export(normalize_counts)
export(olink_analysis)
export(olink_count_table)
export(olink_filtering)
export(olink_info)
export(olink_lod_qc)
export(olink_odds_ratios)
export(olink_pca_outliers)
export(olink_umap_outliers)
export(one_hot_encode_ovr)
export(ovr_deseq_results)
export(pairwise_combos)
export(plot_clinical_factors_heatmap)
export(plot_correlation_matrix)
export(plot_enrichment_terms)
export(plot_forest)
export(plot_stratified_forest)
export(plot_volcano)
export(prep_nmf_data)
export(rna_enrichment)
export(rna_preprocessing)
export(rowData)
export(run_deseq)
export(run_limma)
export(save_gse)
export(save_se)
export(select_top_expression)
export(select_top_lasso)
export(select_top_variability)
export(stats_table)
export(stratified_enrichr)
export(stratified_ora)
export(summarize_experiment)
export(survival_analysis)
export(theme_matt)
export(time_function)
import(ggplot2)
importFrom(AnnotationDbi,mapIds)
importFrom(BiocManager,install)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,HeatmapAnnotation)
importFrom(DESeq2,DESeq)
importFrom(DESeq2,DESeqDataSet)
importFrom(DESeq2,counts)
importFrom(DESeq2,estimateSizeFactors)
importFrom(DESeq2,lfcShrink)
importFrom(DESeq2,plotMA)
importFrom(DESeq2,results)
importFrom(DESeq2,rlog)
importFrom(DESeq2,sizeFactors)
importFrom(DESeq2,varianceStabilizingTransformation)
importFrom(DESeq2,vst)
importFrom(EnhancedVolcano,EnhancedVolcano)
importFrom(NMF,nmf)
importFrom(NMF,randomize)
importFrom(OlinkAnalyze,olink_pathway_enrichment)
importFrom(OlinkAnalyze,olink_pathway_heatmap)
importFrom(OlinkAnalyze,olink_pathway_visualization)
importFrom(OlinkAnalyze,olink_pca_plot)
importFrom(OlinkAnalyze,olink_umap_plot)
importFrom(OlinkAnalyze,olink_volcano_plot)
importFrom(OlinkAnalyze,olink_wilcox)
importFrom(RColorBrewer,brewer.pal)
importFrom(S4Vectors,DataFrame)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(broom,tidy)
importFrom(circlize,colorRamp2)
importFrom(clusterProfiler,GSEA)
importFrom(clusterProfiler,enrichGO)
importFrom(clusterProfiler,enrichKEGG)
importFrom(clusterProfiler,groupGO)
importFrom(clusterProfiler,gseGO)
importFrom(cowplot,plot_grid)
importFrom(dplyr,"%>%")
importFrom(dplyr,across)
importFrom(dplyr,add_row)
importFrom(dplyr,any_of)
importFrom(dplyr,arrange)
importFrom(dplyr,as_tibble)
importFrom(dplyr,bind_rows)
importFrom(dplyr,case_when)
importFrom(dplyr,everything)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,inner_join)
importFrom(dplyr,mutate)
importFrom(dplyr,n_distinct)
importFrom(dplyr,pull)
importFrom(dplyr,rowwise)
importFrom(dplyr,select)
importFrom(dplyr,select_if)
importFrom(dplyr,slice)
importFrom(dplyr,starts_with)
importFrom(dplyr,summarise)
importFrom(dplyr,summarise_all)
importFrom(dplyr,sym)
importFrom(dplyr,ungroup)
importFrom(dplyr,where)
importFrom(edgeR,calcNormFactors)
importFrom(edgeR,cpm)
importFrom(edgeR,filterByExpr)
importFrom(edgeR,rpkm)
importFrom(enrichR,enrichr)
importFrom(enrichplot,cnetplot)
importFrom(enrichplot,dotplot)
importFrom(enrichplot,heatplot)
importFrom(enrichplot,ridgeplot)
importFrom(forcats,fct_reorder)
importFrom(ggbiplot,ggbiplot)
importFrom(ggplot2,aes)
importFrom(ggplot2,annotate)
importFrom(ggplot2,coord_cartesian)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_col)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,guide_colorbar)
importFrom(ggplot2,labs)
importFrom(ggplot2,lims)
importFrom(ggplot2,scale_fill_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_classic)
importFrom(ggpubr,stat_compare_means)
importFrom(ggpubr,stat_cor)
importFrom(ggpubr,theme_classic2)
importFrom(ggrepel,geom_text_repel)
importFrom(ggsci,pal_npg)
importFrom(ggsurvfit,add_confidence_interval)
importFrom(ggsurvfit,ggsurvfit)
importFrom(ggtree,geom_tiplab)
importFrom(ggtree,ggtree)
importFrom(ggtree,theme_tree2)
importFrom(glmnet,cv.glmnet)
importFrom(glue,glue)
importFrom(jsonlite,fromJSON)
importFrom(jsonlite,toJSON)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,topTable)
importFrom(msigdbr,msigdbr)
importFrom(org.Hs.eg.db,org.Hs.eg.db)
importFrom(parallel,detectCores)
importFrom(parallel,makeCluster)
importFrom(parallel,stopCluster)
importFrom(purrr,map)
importFrom(purrr,map_dfr)
importFrom(purrr,reduce)
importFrom(rlang,"!!")
importFrom(rlang,sym)
importFrom(rstatix,anova_test)
importFrom(rstatix,cor_test)
importFrom(rstatix,t_test)
importFrom(rstatix,wilcox_test)
importFrom(singscore,rankGenes)
importFrom(stringr,str_split)
importFrom(stringr,str_wrap)
importFrom(survival,Surv)
importFrom(survival,coxph)
importFrom(survival,survdiff)
importFrom(survival,survfit)
importFrom(tableone,CreateTableOne)
importFrom(tibble,column_to_rownames)
importFrom(tibble,rownames_to_column)
importFrom(tidyr,any_of)
importFrom(tidyr,drop_na)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,pivot_wider)