PRONE/NAMESPACE at main · daisybio/PRONE · GitHub

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# Generated by roxygen2: do not edit by hand

export(apply_thresholds)
export(check_input_assays)
export(check_plot_DE_parameters)
export(check_stats_spiked_DE_parameters)
export(detect_outliers_POMA)
export(eigenMSNorm)
export(export_data)
export(express_to_DT)
export(extract_consensus_DE_candidates)
export(filter_out_NA_proteins_by_threshold)
export(filter_out_complete_NA_proteins)
export(filter_out_proteins_by_ID)
export(filter_out_proteins_by_value)
export(get_NA_overview)
export(get_color_value)
export(get_condition_value)
export(get_facet_value)
export(get_label_value)
export(get_normalization_methods)
export(get_overview_DE)
export(get_proteins_by_value)
export(get_shape_value)
export(get_spiked_stats_DE)
export(globalIntNorm)
export(globalMeanNorm)
export(globalMedianNorm)
export(impute_se)
export(irsNorm)
export(limmaNorm)
export(load_data)
export(load_spike_data)
export(loessCycNorm)
export(loessFNorm)
export(meanNorm)
export(medianAbsDevNorm)
export(medianNorm)
export(normalize_se)
export(normalize_se_combination)
export(normalize_se_single)
export(normicsNorm)
export(plot_NA_density)
export(plot_NA_frequency)
export(plot_NA_heatmap)
export(plot_PCA)
export(plot_ROC_AUC_spiked)
export(plot_TP_FP_spiked_bar)
export(plot_TP_FP_spiked_box)
export(plot_TP_FP_spiked_scatter)
export(plot_boxplots)
export(plot_condition_overview)
export(plot_densities)
export(plot_fold_changes_spiked)
export(plot_heatmap)
export(plot_heatmap_DE)
export(plot_histogram_spiked)
export(plot_identified_spiked_proteins)
export(plot_intersection_enrichment)
export(plot_intragroup_PCV)
export(plot_intragroup_PEV)
export(plot_intragroup_PMAD)
export(plot_intragroup_correlation)
export(plot_jaccard_heatmap)
export(plot_logFC_thresholds_spiked)
export(plot_markers_boxplots)
export(plot_nr_prot_samples)
export(plot_overview_DE_bar)
export(plot_overview_DE_tile)
export(plot_profiles_spiked)
export(plot_pvalues_spiked)
export(plot_stats_spiked_heatmap)
export(plot_tot_int_samples)
export(plot_upset)
export(plot_upset_DE)
export(plot_volcano_DE)
export(quantileNorm)
export(readPRONE_example)
export(remove_POMA_outliers)
export(remove_assays_from_SE)
export(remove_reference_samples)
export(remove_samples_manually)
export(rlrMACycNorm)
export(rlrMANorm)
export(rlrNorm)
export(robnormNorm)
export(run_DE)
export(specify_comparisons)
export(subset_SE_by_norm)
export(tib_to_DF)
export(tmmNorm)
export(vsnNorm)
importFrom(MSnbase,MSnSet)
importFrom(SummarizedExperiment,assay)
importFrom(ggtext,element_textbox_simple)
importFrom(magrittr,"%>%")