NAMESPACE

# Generated by roxygen2: do not edit by hand

S3method(print,parcutils)
S3method(print,parcutils_ase)
S3method(print,parcutils_ir)
export(.assign_class_irFinderSdata)
export(.check_mendate_columns_for_irFinderSdata)
export(.count_data_convert_NA_to_0)
export(.dsr_to_tibble)
export(.filter_df_by_genes)
export(.filter_orgdb_by_genetype)
export(.filter_rows_from_count_data)
export(.fix_ASE_diff_rslt_columns)
export(.fix_hm_colors)
export(.generate_a_lineplot)
export(.generate_go_emap_plot)
export(.get_all_expressed_genes)
export(.get_all_named_expression_matrix)
export(.get_count_data)
export(.get_gene_groups_for_fc_scatter_plot)
export(.get_intron_annotations)
export(.get_parcutils_obj_gene_names)
export(.get_parcutils_object_example)
export(.get_replicates_by_sample_list)
export(.get_sample_information)
export(.group_replicates_by_sample)
export(.is_genes_present_in_obj_parcutils)
export(.is_sample_comparsions_present_in_obj_parcutils)
export(.keep_only_enriched_go)
export(.map_granges_metadata)
export(.parallel_import_bw_files)
export(.parcutils_assign_intron_identifier)
export(.perform_kemans_cluster)
export(.piarwise_upset)
export(.prepare_parcutils_ir)
export(.save_de_ir_results)
export(.save_deg_results)
export(.simplify_go)
export(.validate_a_list_of_normalised_matrix)
export(.validate_irfinders_object)
export(.validate_parcutils_ir_object)
export(.validate_parcutils_obj)
export(EnhancedVolcano2)
export(enrichMsigDB)
export(event_region_to_coordinate)
export(event_region_to_granges)
export(get_ASE_by_regulation)
export(get_ASE_counts_barplot)
export(get_ASE_data_matrix)
export(get_ASEsets_by_regulation)
export(get_ase_data_matrix_heatmap)
export(get_ase_volcano_plot)
export(get_chip_signal_heatmap)
export(get_chip_signal_over_control_heatmap)
export(get_corr_heatbox)
export(get_diff_ASE_count_barplot)
export(get_diff_gene_count_barplot)
export(get_event_annotations)
export(get_five_prime_flank_motif)
export(get_fold_change_heatmap)
export(get_fold_change_line_plot)
export(get_fold_change_matrix)
export(get_fold_change_scatter_plot)
export(get_gene_expression_box_plot)
export(get_gene_expression_heatmap)
export(get_gene_expression_line_plot)
export(get_genes_by_regulation)
export(get_genes_from_event_name)
export(get_genesets_by_regulation)
export(get_go_emap_plot)
export(get_heatmap_data)
export(get_intergenic_signals)
export(get_normalised_expression_matrix)
export(get_pairwise_corr_plot)
export(get_pca_plot)
export(get_star_align_log_summary)
export(get_star_align_log_summary_plot)
export(get_three_prime_flank_motif)
export(get_upset_intersects)
export(get_volcano_plot)
export(ggsave2)
export(gseMsigDB)
export(gsea_analysis)
export(import_topn_bed_features)
export(make_enriched_heatmap_list)
export(make_parcutils_chip)
export(named_group_split)
export(normalise_counts)
export(normalised_matrix_to_rpm)
export(parcutils_chip)
export(plot_chip_pairwise_correlation_heatmap)
export(plot_deASE_venn)
export(plot_deg_upsets)
export(plot_deg_venn)
export(plot_regions_relative_to_reference)
export(print.parcutils)
export(print.parcutils_ase)
export(print.parcutils_ir)
export(run_ase_diff_analysis)
export(run_deseq_analysis)
export(save_go_data)
export(save_go_plots)
export(sort_geom_box)
exportClasses(parcutils_chip)
import(ComplexHeatmap)
import(DESeq2)
import(EnrichedHeatmap)
import(clusterProfiler)
import(dplyr)
import(ggcorrplot)
import(ggeasy)
import(msigdbr)
import(org.Mm.eg.db)
import(scales)
import(tidyselect)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,binnedAverage)
importFrom(GenomicRanges,gaps)
importFrom(GenomicRanges,mcolAsRleList)
importFrom(dplyr,arrange)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,mutate)
importFrom(dplyr,pull)
importFrom(dplyr,summarise)
importFrom(ggvenn,ggvenn)
importFrom(magrittr,"%>%")
importFrom(purrr,map2)
importFrom(purrr,map_lgl)
importFrom(rlang,`!!!`)
importFrom(rlang,expr)
importFrom(rlang,inject)
importFrom(rtracklayer,import)
importFrom(stringr,str_c)
importFrom(tibble,as_tibble)
importFrom(tidyselect,everything)
importFrom(tools,file_path_sans_ext)
importFrom(viridis,viridis)
importFrom(writexl,write_xlsx)