NAMESPACE

# Generated by roxygen2: do not edit by hand

S3method("[",expt)
S3method(print,abundant_genes)
S3method(print,all_gprofiler)
S3method(print,all_pairwise)
S3method(print,annotations_biomart)
S3method(print,aucc_info)
S3method(print,biomart_go)
S3method(print,cds_variant_primers)
S3method(print,classified_mutations)
S3method(print,classifier_evaluation)
S3method(print,clusterprofiler_result)
S3method(print,combined_de)
S3method(print,combined_de_upset)
S3method(print,combined_table)
S3method(print,correlation_heatmap)
S3method(print,cross_table_comparison)
S3method(print,density_plot)
S3method(print,density_primers)
S3method(print,deseq_lrt)
S3method(print,distance_heatmap)
S3method(print,dream_pairwise)
S3method(print,expt)
S3method(print,goseq_result)
S3method(print,gostats_result)
S3method(print,gprofiler_result)
S3method(print,graphed_metrics)
S3method(print,gsva_result)
S3method(print,gsva_sig)
S3method(print,legend_plot)
S3method(print,libsize_plot)
S3method(print,mapped_keepers)
S3method(print,meta_sankey)
S3method(print,nonzero_plot)
S3method(print,partitioned_data)
S3method(print,pattern_counted)
S3method(print,pca_result)
S3method(print,prepost_filter)
S3method(print,preprocessing_metadata)
S3method(print,proper_estimate)
S3method(print,reordered_varpart)
S3method(print,sig_genes)
S3method(print,sig_intersect)
S3method(print,snp_intersections)
S3method(print,snp_sets)
S3method(print,snps_genes)
S3method(print,standardmedian_plot)
S3method(print,topgo_result)
S3method(print,topn_plot)
S3method(print,varcoef_plot)
S3method(print,varpart)
S3method(print,written_expt)
S3method(print,written_xlsx)
export("%>%")
export("%dopar%")
export(":=")
export("colors<-")
export(add_clonotype_annotations)
export(add_conditional_nas)
export(all_adjusters)
export(all_cprofiler)
export(all_gprofiler)
export(all_ontology_searches)
export(all_pairwise)
export(basic_pairwise)
export(batch_counts)
export(binary_pairwise)
export(bioc_all)
export(calculate_aucc)
export(cbcb_batch)
export(cbcb_combat)
export(cbcb_filter_counts)
export(check_metadata_year)
export(choose_dataset)
export(choose_model)
export(circos_arc)
export(circos_heatmap)
export(circos_hist)
export(circos_ideogram)
export(circos_karyotype)
export(circos_make)
export(circos_plus_minus)
export(circos_prefix)
export(circos_suffix)
export(circos_ticks)
export(circos_tile)
export(classify_n_times)
export(classify_variants)
export(clear_session)
export(cleavage_histogram)
export(cluster_trees)
export(colors)
export(combine_de_tables)
export(combine_expts)
export(compare_de_results)
export(compare_de_tables)
export(compare_go_searches)
export(compare_logfc_plots)
export(compare_significant_contrasts)
export(compare_surrogate_estimates)
export(concatenate_runs)
export(convert_counts)
export(convert_gsc_ids)
export(convert_ids)
export(cordist)
export(correlate_de_tables)
export(count_clonotype_by_cluster)
export(count_expt_snps)
export(count_nmer)
export(counts_from_surrogates)
export(create_expt)
export(create_partitions)
export(create_scd)
export(create_se)
export(de_venn)
export(deparse_go_value)
export(deseq2_pairwise)
export(deseq_lrt)
export(deseq_pairwise)
export(divide_seq)
export(do_pairwise)
export(do_topgo)
export(download_gbk)
export(dream_pairwise)
export(ebseq_pairwise)
export(edger_pairwise)
export(exclude_genes_expt)
export(expt)
export(extract_abundant_genes)
export(extract_coefficient_scatter)
export(extract_de_plots)
export(extract_eupath_orthologs)
export(extract_go)
export(extract_lengths)
export(extract_linear_regression)
export(extract_logistic_regression)
export(extract_mayu_pps_fdr)
export(extract_metadata)
export(extract_msraw_data)
export(extract_mzML_scans)
export(extract_mzXML_scans)
export(extract_peprophet_data)
export(extract_pyprophet_data)
export(extract_scan_data)
export(extract_siggenes)
export(extract_significant_genes)
export(factor_rsquared)
export(features_greater_than)
export(features_in_single_condition)
export(features_less_than)
export(filter_counts)
export(filter_scd)
export(find_working_dataset)
export(find_working_mart)
export(gather_ontology_genes)
export(gather_preprocessing_metadata)
export(gather_utrs_padding)
export(genefilter_cv_counts)
export(genefilter_kofa_counts)
export(genefilter_pofa_counts)
export(generate_nn_groups)
export(genomic_kmer_dist)
export(genoplot_chromosome)
export(getEdgeWeights)
export(get_abundant_genes)
export(get_expt_colors)
export(get_formula_factors)
export(get_genesizes)
export(get_git_commit)
export(get_group_gsva_means)
export(get_gsvadb_names)
export(get_kegg_compounds)
export(get_kegg_genes)
export(get_kegg_orgn)
export(get_kegg_sub)
export(get_microbesonline_taxid)
export(get_msigdb_metadata)
export(get_pairwise_gene_abundances)
export(get_proportion_snp_sets)
export(get_sig_genes)
export(get_sig_gsva_categories)
export(get_snp_sets)
export(get_yyyymm_commit)
export(gff2gr)
export(gff2irange)
export(ggplotly_url)
export(ggplt)
export(godef)
export(golev)
export(golevel)
export(golevel_df)
export(goont)
export(gosec)
export(goseq2enrich)
export(goseq_msigdb)
export(goseq_table)
export(goseq_trees)
export(gostats2enrich)
export(gostats_kegg)
export(gostats_trees)
export(gosyn)
export(goterm)
export(gotest)
export(gprofiler2enrich)
export(graph_metrics)
export(group_mean_cds_length)
export(guess_orgdb_keytype)
export(heatmap.3)
export(hpgl_GOplot)
export(hpgl_arescore)
export(hpgl_cor)
export(hpgl_dist)
export(hpgl_filter_counts)
export(hpgl_log2cpm)
export(hpgl_norm)
export(hpgl_padjust)
export(hpgl_qshrink)
export(hpgl_qstats)
export(hpgl_rpkm)
export(hpgl_voom)
export(hpgl_voomweighted)
export(iDA)
export(impute_expt)
export(init_xlsx)
export(intersect_signatures)
export(intersect_significant)
export(iterate_linear_regression)
export(iterate_logistic_regression)
export(limma_pairwise)
export(load_annotations)
export(load_biomart_annotations)
export(load_biomart_go)
export(load_biomart_orthologs)
export(load_genbank_annotations)
export(load_gff_annotations)
export(load_gmt_signatures)
export(load_kegg_annotations)
export(load_microbesonline_annotations)
export(load_microbesonline_go)
export(load_orgdb_annotations)
export(load_orgdb_go)
export(load_trinotate_annotations)
export(load_trinotate_go)
export(load_uniprot_annotations)
export(load_uniprot_go)
export(loadme)
export(make_assembly_spec)
export(make_dnaseq_spec)
export(make_gsc_from_abundant)
export(make_gsc_from_ids)
export(make_gsc_from_pairwise)
export(make_id2gomap)
export(make_ntile_factor)
export(make_pairwise_contrasts)
export(make_pombe_expt)
export(make_pombe_se)
export(make_quartile_factor)
export(make_rnaseq_spec)
export(make_simplified_contrast_matrix)
export(make_tx_gene_map)
export(map_kegg_dbs)
export(map_orgdb_ids)
export(mean_by_bioreplicate)
export(mean_by_factor)
export(median_by_factor)
export(mesg)
export(myretrieveKGML)
export(noiseq_pairwise)
export(normalize_counts)
export(normalize_expt)
export(normalize_se)
export(orgdb_from_ah)
export(overlap_geneids)
export(overlap_groups)
export(pattern_count_genome)
export(pc_fstatistics)
export(pca_highscores)
export(pca_information)
export(pct_all_kegg)
export(pct_kegg_diff)
export(plot_3d_pca)
export(plot_batchsv)
export(plot_bcv)
export(plot_boxplot)
export(plot_cleaved)
export(plot_corheat)
export(plot_density)
export(plot_disheat)
export(plot_dist_scatter)
export(plot_epitrochoid)
export(plot_essentiality)
export(plot_exprs_by_chromosome)
export(plot_forest_from_regression)
export(plot_fun_venn)
export(plot_goseq_pval)
export(plot_gostats_pval)
export(plot_gprofiler2_pval)
export(plot_gprofiler_pval)
export(plot_heatmap)
export(plot_heatplus)
export(plot_histogram)
export(plot_hypotrochoid)
export(plot_intensity_mz)
export(plot_legend)
export(plot_libsize)
export(plot_libsize_prepost)
export(plot_linear_scatter)
export(plot_ma_de)
export(plot_meta_sankey)
export(plot_metadata_factors)
export(plot_multihistogram)
export(plot_multiplot)
export(plot_mzxml_boxplot)
export(plot_nonzero)
export(plot_num_siggenes)
export(plot_ontpval)
export(plot_pairwise_ma)
export(plot_pca)
export(plot_pca_genes)
export(plot_pcfactor)
export(plot_pcload)
export(plot_pcs)
export(plot_pct_kept)
export(plot_peprophet_data)
export(plot_pyprophet_counts)
export(plot_pyprophet_distribution)
export(plot_pyprophet_points)
export(plot_pyprophet_protein)
export(plot_pyprophet_xy)
export(plot_qq_all)
export(plot_rmats)
export(plot_sample_cvheatmap)
export(plot_sample_heatmap)
export(plot_scatter)
export(plot_seurat_scatter)
export(plot_significant_bar)
export(plot_single_qq)
export(plot_sm)
export(plot_spirograph)
export(plot_suppa)
export(plot_svfactor)
export(plot_topgo_densities)
export(plot_topgo_pval)
export(plot_topn)
export(plot_topn_gsea)
export(plot_tsne)
export(plot_variance_coefficients)
export(plot_volcano_condition_de)
export(plot_volcano_de)
export(plotly_pca)
export(pp)
export(print_ups_downs)
export(pull_git_commit)
export(random_ontology)
export(rank_order_scatter)
export(read_counts_expt)
export(read_metadata)
export(read_thermo_xlsx)
export(record_seurat_samples)
export(renderme)
export(replot_varpart_percent)
export(rex)
export(rowmax_filter_counts)
export(s2s_all_filters)
export(sanitize_expt_fData)
export(sanitize_expt_pData)
export(sanitize_metadata)
export(sanitize_percent)
export(saveme)
export(score_gsva_likelihoods)
export(self_evaluate_model)
export(semantic_copynumber_extract)
export(semantic_copynumber_filter)
export(semantic_expt_filter)
export(sequence_attributes)
export(set_expt_batches)
export(set_expt_colors)
export(set_expt_conditions)
export(set_expt_factors)
export(set_expt_genename_column)
export(set_expt_genenames)
export(set_expt_samplenames)
export(significant_barplots)
export(sillydist)
export(simple_clusterprofiler)
export(simple_cprofiler)
export(simple_dorothea)
export(simple_filter_counts)
export(simple_gadem)
export(simple_goseq)
export(simple_gostats)
export(simple_gprofiler)
export(simple_gprofiler2)
export(simple_gsva)
export(simple_pathview)
export(simple_proper)
export(simple_topgo)
export(simple_varpart)
export(simple_xcell)
export(skim_seurat_metadata)
export(slide_de_threshold)
export(sm)
export(snp_density_primers)
export(snp_subset_genes)
export(snps_intersections)
export(snps_vs_genes)
export(snps_vs_genes_padded)
export(steal_salmon_tx_ids)
export(subset_expt)
export(subset_genes)
export(subset_ontology_search)
export(subtract_expt)
export(sum_exon_widths)
export(sv_fstatistics)
export(svpc_fstats)
export(tar_meta_column)
export(tempfile)
export(test_design_model_rank)
export(test_model_rank)
export(tmpmd5file)
export(tnseq_multi_saturation)
export(tnseq_saturation)
export(topDiffGenes)
export(topgo_tables)
export(topgo_trees)
export(transform_counts)
export(u_plot)
export(unAsIs)
export(upsetr_combined_de)
export(upsetr_sig)
export(variance_expt)
export(what_happened)
export(write_basic)
export(write_cds_entries)
export(write_classifier_summary)
export(write_cp_data)
export(write_de_table)
export(write_density_primers)
export(write_deseq)
export(write_edger)
export(write_expt)
export(write_go_xls)
export(write_goseq_data)
export(write_gostats_data)
export(write_gprofiler_data)
export(write_gsva)
export(write_limma)
export(write_snps)
export(write_subset_ontologies)
export(write_suppa_table)
export(write_svpc_fstats)
export(write_topgo_data)
export(write_varpart)
export(write_xlsx)
export(xlsx_insert_png)
export(ymxb_print)
exportMethods("[[")
exportMethods("annotation<-")
exportMethods("assay<-")
exportMethods("colData<-")
exportMethods("colors<-")
exportMethods("exprs<-")
exportMethods("fData<-")
exportMethods("pData<-")
exportMethods("rowData<-")
exportMethods("sampleNames<-")
exportMethods("state<-")
exportMethods(annotation)
exportMethods(assay)
exportMethods(backup_expression_data)
exportMethods(colData)
exportMethods(colors)
exportMethods(count_nmer)
exportMethods(exprs)
exportMethods(extract_keepers)
exportMethods(fData)
exportMethods(get_backup_expression_data)
exportMethods(get_formula_factors)
exportMethods(iDA)
exportMethods(normalize_expt)
exportMethods(notes)
exportMethods(pData)
exportMethods(plot_heatmap)
exportMethods(plot_libsize)
exportMethods(plot_meta_sankey)
exportMethods(plot_nonzero)
exportMethods(plot_sample_heatmap)
exportMethods(plot_sm)
exportMethods(plot_topn_gsea)
exportMethods(plot_variance_coefficients)
exportMethods(rowData)
exportMethods(sampleNames)
exportMethods(state)
exportMethods(subset_expt)
exportMethods(tar_meta_column)
exportMethods(test_design_model_rank)
exportMethods(write_xlsx)
import(Biobase)
import(broom)
import(grDevices)
import(graphics)
import(methods)
import(shiny)
import(utils)
importClassesFrom(DOSE,enrichResult)
importFrom(Biobase,"annotation<-")
importFrom(Biobase,annotation)
importFrom(Biobase,exprs)
importFrom(Biobase,fData)
importFrom(Biobase,notes)
importFrom(Biobase,pData)
importFrom(Biobase,sampleNames)
importFrom(GSEABase,GeneColorSet)
importFrom(GSEABase,GeneSet)
importFrom(IRanges,"%over%")
importFrom(RSQLite,dbClearResult)
importFrom(RSQLite,dbConnect)
importFrom(RSQLite,dbFetch)
importFrom(RSQLite,dbSendQuery)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,mcols)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"metadata<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(data.table,":=")
importFrom(data.table,data.table)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,n)
importFrom(dplyr,summarise)
importFrom(dplyr,vars)
importFrom(foreach,"%dopar%")
importFrom(foreach,foreach)
importFrom(ggplot2,aes)
importFrom(ggplot2,element_text)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,theme)
importFrom(glue,glue)
importFrom(glue,glue_data)
importFrom(grDevices,recordPlot)
importFrom(magrittr,"%>%")
importFrom(plotly,plot_ly)
importFrom(rlang,.data)
importFrom(rlang,abort)
importFrom(rlang,sym)
importFrom(stats,aggregate)
importFrom(stats,as.dendrogram)
importFrom(stats,as.formula)
importFrom(stats,ave)
importFrom(stats,biplot)
importFrom(stats,coef)
importFrom(stats,coefficients)
importFrom(stats,complete.cases)
importFrom(stats,cor)
importFrom(stats,cor.test)
importFrom(stats,density)
importFrom(stats,dist)
importFrom(stats,dnorm)
importFrom(stats,formula)
importFrom(stats,glm)
importFrom(stats,hclust)
importFrom(stats,lm)
importFrom(stats,lowess)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,na.omit)
importFrom(stats,order.dendrogram)
importFrom(stats,p.adjust)
importFrom(stats,p.adjust.methods)
importFrom(stats,pnorm)
importFrom(stats,princomp)
importFrom(stats,quantile)
importFrom(stats,relevel)
importFrom(stats,reorder)
importFrom(stats,resid)
importFrom(stats,residuals)
importFrom(stats,rnbinom)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,t.test)
importFrom(stats,var)
importFrom(tidyselect,all_of)
importMethodsFrom(Matrix,rowMeans)