# Generated by roxygen2: do not edit by hand

export(HaDeX_GUI)
export(HaDeXify)
export(add_stat_dependency)
export(calculate_MHP)
export(calculate_aggregated_diff_uptake)
export(calculate_aggregated_test_results)
export(calculate_aggregated_uptake)
export(calculate_auc)
export(calculate_back_exchange)
export(calculate_confidence_limit_values)
export(calculate_diff_uptake)
export(calculate_exp_masses)
export(calculate_exp_masses_per_replicate)
export(calculate_kinetics)
export(calculate_p_value)
export(calculate_peptide_kinetics)
export(calculate_state_uptake)
export(create_aggregated_diff_uptake_dataset)
export(create_aggregated_uptake_dataset)
export(create_control_dataset)
export(create_diff_uptake_dataset)
export(create_kinetic_dataset)
export(create_overlap_distribution_dataset)
export(create_p_diff_uptake_dataset)
export(create_p_diff_uptake_dataset_with_confidence)
export(create_quality_control_dataset)
export(create_replicate_dataset)
export(create_state_comparison_dataset)
export(create_state_uptake_dataset)
export(create_uptake_dataset)
export(get_n_replicates)
export(get_peptide_sequence)
export(get_protein_coverage)
export(get_protein_redundancy)
export(get_replicate_list_sd)
export(get_residue_positions)
export(get_structure_color)
export(install_GUI)
export(plot_aggregated_differential_uptake)
export(plot_aggregated_uptake)
export(plot_aggregated_uptake_structure)
export(plot_amino_distribution)
export(plot_butterfly)
export(plot_chiclet)
export(plot_coverage)
export(plot_coverage_heatmap)
export(plot_differential)
export(plot_differential_butterfly)
export(plot_differential_chiclet)
export(plot_differential_uptake_curve)
export(plot_manhattan)
export(plot_overlap)
export(plot_overlap_distribution)
export(plot_peptide_charge_measurement)
export(plot_peptide_mass_measurement)
export(plot_position_frequency)
export(plot_quality_control)
export(plot_replicate_histogram)
export(plot_replicate_mass_uptake)
export(plot_state_comparison)
export(plot_uncertainty)
export(plot_uptake_curve)
export(plot_volcano)
export(prepare_hdxviewer_export)
export(read_hdx)
export(reconstruct_sequence)
export(show_aggregated_uptake_data)
export(show_coverage_heatmap_data)
export(show_diff_uptake_data)
export(show_diff_uptake_data_confidence)
export(show_overlap_data)
export(show_p_diff_uptake_data)
export(show_peptide_charge_measurement)
export(show_peptide_mass_measurement)
export(show_quality_control_data)
export(show_replicate_histogram_data)
export(show_summary_data)
export(show_uc_data)
export(show_uptake_data)
export(update_hdexaminer_file)
importFrom(checkmate,assert)
importFrom(checkmate,assert_data_frame)
importFrom(checkmate,assert_number)
importFrom(checkmate,assert_string)
importFrom(data.table,":=")
importFrom(data.table,`:=`)
importFrom(data.table,as.data.table)
importFrom(data.table,data.table)
importFrom(data.table,dcast)
importFrom(data.table,fcase)
importFrom(data.table,fcoalesce)
importFrom(data.table,fifelse)
importFrom(data.table,fread)
importFrom(data.table,melt.data.table)
importFrom(data.table,merge.data.table)
importFrom(data.table,rbindlist)
importFrom(data.table,setattr)
importFrom(data.table,setcolorder)
importFrom(data.table,setnames)
importFrom(data.table,setorderv)
importFrom(data.table,tstrsplit)
importFrom(data.table,uniqueN)
importFrom(dplyr,"%>%")
importFrom(dplyr,arrange)
importFrom(dplyr,bind_rows)
importFrom(dplyr,case_when)
importFrom(dplyr,coalesce)
importFrom(dplyr,cur_group_id)
importFrom(dplyr,everything)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,pull)
importFrom(dplyr,rename)
importFrom(dplyr,right_join)
importFrom(dplyr,select)
importFrom(dplyr,summarise)
importFrom(dplyr,summarize)
importFrom(dplyr,ungroup)
importFrom(ggiraph,geom_col_interactive)
importFrom(ggiraph,geom_point_interactive)
importFrom(ggiraph,geom_rect_interactive)
importFrom(ggiraph,geom_segment_interactive)
importFrom(ggiraph,geom_tile_interactive)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,annotate)
importFrom(ggplot2,annotation_custom)
importFrom(ggplot2,coord_cartesian)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_col)
importFrom(ggplot2,geom_density)
importFrom(ggplot2,geom_errorbar)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_rect)
importFrom(ggplot2,geom_ribbon)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggplot_build)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_colour_discrete)
importFrom(ggplot2,scale_colour_identity)
importFrom(ggplot2,scale_fill_gradient2)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_linetype_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_x_log10)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(glue,glue)
importFrom(grid,rasterGrob)
importFrom(gridExtra,grid.arrange)
importFrom(magick,image_read)
importFrom(purrr,map_chr)
importFrom(r3dmol,m_add_model)
importFrom(r3dmol,m_set_style)
importFrom(r3dmol,m_style_cartoon)
importFrom(r3dmol,m_zoom_to)
importFrom(r3dmol,r3dmol)
importFrom(readr,col_character)
importFrom(readr,cols)
importFrom(readr,parse_character)
importFrom(readr,parse_double)
importFrom(readr,parse_integer)
importFrom(readr,parse_logical)
importFrom(readr,parse_number)
importFrom(readr,read_csv)
importFrom(readr,read_tsv)
importFrom(readxl,read_excel)
importFrom(remotes,install_github)
importFrom(stats,qt)
importFrom(stringi,stri_count)
importFrom(stringi,stri_count_fixed)
importFrom(tidyr,gather)
importFrom(tidyr,replace_na)
importFrom(tidyr,spread)
importFrom(tidyr,unite)
importFrom(tools,file_ext)
importFrom(utils,packageVersion)
importFrom(utils,write.csv)
