PRONE-package	PRONE-package
apply_thresholds	apply_thresholds
check_DEqMS_parameter	check_DEqMS_parameter
check_DE_parameters	check_DE_parameters
check_input_assays	check_input_assays
check_plot_DE_parameters	check_plot_DE_parameters
check_stats_spiked_DE_parameters	check_stats_spiked_DE_parameters
detect_outliers_POMA	detect_outliers_POMA
eigenMSNorm	eigenMSNorm
export_data	export_data
express_to_DT	express_to_DT
extract_consensus_DE_candidates	extract_consensus_DE_candidates
extract_limma_DE	extract_limma_DE
filter_out_complete_NA_proteins	filter_out_complete_NA_proteins
filter_out_NA_proteins_by_threshold	filter_out_NA_proteins_by_threshold
filter_out_proteins_by_ID	filter_out_proteins_by_ID
filter_out_proteins_by_value	filter_out_proteins_by_value
get_color_value	get_color_value
get_complete_dt	get_complete_dt
get_complete_pca_dt	get_complete_pca_dt
get_condition_value	get_condition_value
get_facet_value	get_facet_value
get_label_value	get_label_value
get_NA_overview	get_NA_overview
get_normalization_methods	get_normalization_methods
get_overview_DE	get_overview_DE
get_proteins_by_value	get_proteins_by_value
get_shape_value	get_shape_value
get_spiked_stats_DE	get_spiked_stats_DE
globalIntNorm	globalIntNorm
globalMeanNorm	globalMeanNorm
globalMedianNorm	globalMedianNorm
impute_se	impute_se
irsNorm	irsNorm
limmaNorm	limmaNorm
load_data	load_data
load_spike_data	load_spike_data
loessCycNorm	loessCycNorm
loessFNorm	loessFNorm
meanNorm	meanNorm
medianAbsDevNorm	medianAbsDevNorm
medianNorm	medianNorm
normalize_se	normalize_se
normalize_se_combination	normalize_se_combination
normalize_se_single	normalize_se_single
normicsNorm	normicsNorm
perform_DEqMS	perform_DEqMS
perform_limma	perform_limma
perform_ROTS	perform_ROTS
plot_boxplots	plot_boxplots
plot_condition_overview	plot_condition_overview
plot_densities	plot_densities
plot_fold_changes_spiked	plot_fold_changes_spiked
plot_heatmap	plot_heatmap
plot_heatmap_DE	plot_heatmap_DE
plot_histogram_spiked	plot_histogram_spiked
plot_identified_spiked_proteins	plot_identified_spiked_proteins
plot_intersection_enrichment	plot_intersection_enrichment
plot_intragroup_correlation	plot_intragroup_correlation
plot_intragroup_PCV	plot_intragroup_PCV
plot_intragroup_PEV	plot_intragroup_PEV
plot_intragroup_PMAD	plot_intragroup_PMAD
plot_jaccard_heatmap	plot_jaccard_heatmap
plot_logFC_thresholds_spiked	plot_logFC_thresholds_spiked
plot_markers_boxplots	plot_markers_boxplots
plot_NA_density	plot_NA_density
plot_NA_frequency	plot_NA_frequency
plot_NA_heatmap	plot_NA_heatmap
plot_nr_prot_samples	plot_nr_prot_samples
plot_overview_DE_bar	plot_overview_DE_bar
plot_overview_DE_tile	plot_overview_DE_tile
plot_PCA	plot_PCA
plot_profiles_spiked	plot_profiles_spiked
plot_pvalues_spiked	plot_pvalues_spiked
plot_ROC_AUC_spiked	plot_ROC_AUC_spiked
plot_stats_spiked_heatmap	plot_stats_spiked_heatmap
plot_tot_int_samples	plot_tot_int_samples
plot_TP_FP_spiked_bar	plot_TP_FP_spiked_bar
plot_TP_FP_spiked_box	plot_TP_FP_spiked_box
plot_TP_FP_spiked_scatter	plot_TP_FP_spiked_scatter
plot_upset	plot_upset
plot_upset_DE	plot_upset_DE
plot_volcano_DE	plot_volcano_DE
PRONE	PRONE-package
quantileNorm	quantileNorm
readPRONE_example	readPRONE_example
remove_assays_from_SE	remove_assays_from_SE
remove_POMA_outliers	remove_POMA_outliers
remove_reference_samples	remove_reference_samples
remove_samples_manually	remove_samples_manually
rlrMACycNorm	rlrMACycNorm
rlrMANorm	rlrMANorm
rlrNorm	rlrNorm
RobNorm	RobNorm
robnormNorm	robnormNorm
run_DE	run_DE
run_DE_single	run_DE_single
specify_comparisons	specify_comparisons
spectraCounteBayes_DEqMS	spectraCounteBayes_DEqMS
spike_in_de_res	spike_in_de_res
spike_in_se	spike_in_se
subset_SE_by_norm	subset_SE_by_norm
tib_to_DF	tib_to_DF
tmmNorm	tmmNorm
tuberculosis_TMT_de_res	tuberculosis_TMT_de_res
tuberculosis_TMT_se	tuberculosis_TMT_se
vsnNorm	vsnNorm
