##---- ne ----##

ne_sub_directories_core	true:core:directory	none

ne_file_matrix_annotated	true:core:file	none
ne_file_matrix_IDs	true:core:file	none
ne_file_matrix_symbols	true:core:file	none
ne_file_gene_IDs	true:core:file	none
ne_file_gene_symbols	true:core:file	none
ne_deciles	true:core:file	none
ne_quartiles	true:core:file	none

ne_start_plots	true:plot_core:core	none
ne_plot_distribution_of_expression_values	true:plot:optional	ne/plots/ne_distribution_of_expression_values.txt
ne_plot_PCA_contribution_of_components	true:plot:optional	ne/plots/ne_PCA_contributions_of_components.txt
ne_plot_PCA_scatterplot	true:plot:optional	ne/plots/ne_PCA_scatterplot.txt
ne_plot_correlation_analysis_heatmap	true:plot:optional	ne/plots/ne_correlation_analysis_heatmap.txt
ne_plot_most_expressed_genes_tables	true:plot:optional	ne/plots/ne_most_expressed_genes_tables.txt
ne_plot_most_expressed_genes_boxplots	true:plot:optional	ne/plots/ne_most_expressed_genes_boxplots.txt
ne_end_plots	true:plot_core:core	none
ne_run_r	true:plot_core:core	none

ne_start_report	true:report_core:core	none
ne_report_expression	true:report_title:optional	Expression
ne_report_distribution_of_expression_values	true:report_plot:optional	ne/report/ne_distribution_of_expression_values.txt
ne_report_PCA_contribution_of_components	true:report_plot:optional	ne/report/ne_PCA_contributions_of_components.txt
ne_report_PCA_scatterplot	true:report_plot:optional	ne/report/ne_PCA_scatterplot.txt
ne_report_correlation_analysis_heatmap	true:report_plot:optional	ne/report/ne_correlation_analysis_heatmap.txt
ne_report_most_expressed_genes_tables	true:report_plot:optional	ne/report/ne_most_expressed_genes_tables.txt
ne_report_most_expressed_genes_boxplots	true:report_plot:optional	ne/report/ne_most_expressed_genes_boxplots.txt
ne_report_methodology	true:report_title:optional	Methodology
ne_report_core_workflow_methods	true:report_text:optional	methods/ne/core_workflow.txt
ne_report_extras	true:report_title:optional	Extras
ne_report_citation	true:report_text:optional	citation.txt
ne_end_report	true:report_core:core	none


##---- de ----##

de_sub_directories_core	true:core:directory	none

de_file_gene_IDs	true:core:file	none
de_file_gene_IDs_upregulated	true:core:file	none
de_file_gene_IDs_downregulated	true:core:file	none
de_file_gene_IDs_significant	true:core:file	none
de_file_gene_IDs_significant_upregulated	true:core:file	none
de_file_gene_IDs_significant_downregulated	true:core:file	none
de_file_gene_symbols	true:core:file	none
de_file_gene_symbols_upregulated	true:core:file	none
de_file_gene_symbols_downregulated	true:core:file	none
de_file_gene_symbols_significant	true:core:file	none
de_file_gene_symbols_significant_upregulated	true:core:file	none
de_file_gene_symbols_significant_downregulated	true:core:file	none
de_file_annotated	true:core:file	none
de_file_annotated_upregulated	true:core:file	none
de_file_annotated_downregulated	true:core:file	none
de_file_annotated_significant	true:core:file	none
de_file_annotated_significant_upregulated	true:core:file	none
de_file_annotated_significant_downregulated	true:core:file	none

de_analysis_oras	true:statistical:ora	none
de_analysis_ura	true:statistical:ura	none
de_analysis_spatial	true:statistical:spatial	none

de_start_plots	true:plot_core:core	none
de_plot_distribution_of_expression_values	true:plot:optional	de/plots/de_distribution_of_expression_values.txt
de_plot_PCA_contribution_of_components	true:plot:optional	de/plots/de_PCA_contributions_of_components.txt
de_plot_PCA_scatterplot	true:plot:optional	de/plots/de_PCA_scatterplot.txt
de_plot_correlation_analysis_heatmap	true:plot:optional	de/plots/de_correlation_analysis_heatmap.txt
de_plot_most_expressed_genes_tables	false:plot:optional	de/plots/de_most_expressed_genes_tables.txt
de_plot_most_expressed_genes_boxplots	false:plot:optional	de/plots/de_most_expressed_genes_boxplots.txt
de_plot_volcano_plot	true:plot:optional	de/plots/de_volcano_plot.txt
de_plot_MA_plot	true:plot:optional	de/plots/de_MA_plot.txt
de_plot_number_of_significant_genes	true:plot:optional	de/plots/de_number_of_significant_genes.txt
de_plot_significant_genes_heatmap	true:plot:optional	de/plots/de_significant_genes_heatmap.txt
de_plot_most_differential_genes_tables	true:plot:optional	de/plots/de_most_differential_genes_tables.txt
de_plot_most_differential_genes_boxplots	true:plot:optional	de/plots/de_most_differential_genes_boxplots.txt
de_plot_ora_enriched_gene_sets_barchart	true:plot:ora	de/plots/de_ora_enriched_gene_sets_barcharts.txt
de_plot_ora_enriched_gene_sets_ridgeplot	true:plot:ora	de/plots/de_ora_enriched_gene_sets_ridgeplot.txt
de_plot_ora_enriched_gene_sets_boxplots	true:plot:ora	de/plots/de_ora_enriched_gene_sets_boxplots.txt
de_plot_ora_enriched_gene_sets_network_plots	true:plot:ora	de/plots/de_ora_enriched_gene_sets_network_plots.txt
de_plot_ora_underenriched_gene_barcharts	true:plot:ora	de/plots/de_ora_underenriched_gene_sets_barcharts.txt
de_plot_ura_barcharts	true:plot:ura	de/plots/de_ura_barcharts.txt
de_plot_ura_ridgeplot	true:plot:ura	de/plots/de_ura_ridgeplot.txt
de_plot_ura_boxplots	true:plot:ura	de/plots/de_ura_boxplots.txt
de_plot_ura_network_plots	true:plot:ura	de/plots/de_ura_network_plots.txt
de_plot_spatial_enrichment_table	true:plot:spatial	de/plots/de_spatial_enrichment_table.txt
de_plot_spatial_enrichment_distribution_plots	true:plot:spatial	de/plots/de_spatial_enrichment_distribution_plots.txt
de_end_plots	true:plot_core:core	none
de_run_r	true:plot_core:core	none

de_start_report	true:report_core:core	none
de_report_expression	true:report_title:optional	Expression
de_report_distribution_of_expression_values	true:report_plot:optional	de/report/de_distribution_of_expression_values.txt
de_report_PCA_contribution_of_components	true:report_plot:optional	de/report/de_PCA_contributions_of_components.txt
de_report_PCA_scatterplot	true:report_plot:optional	de/report/de_PCA_scatterplot.txt
de_report_correlation_analysis_heatmap	true:report_plot:optional	de/report/de_correlation_analysis_heatmap.txt
de_report_most_expressed_genes_tables	false:report_plot:optional	de/report/de_most_expressed_genes_tables.txt
de_report_most_expressed_genes_boxplots	false:report_plot:optional	de/report/de_most_expressed_genes_boxplots.txt
de_report_differential_expression	true:report_title:optional	Differential Expression
de_report_volcano_plot	true:report_plot:optional	de/report/de_volcano_plot.txt
de_report_MA_plot	true:report_plot:optional	de/report/de_MA_plot.txt
de_report_number_of_significant_genes	true:report_plot:optional	de/report/de_number_of_significant_genes.txt
de_report_significant_genes_heatmap	true:report_plot:optional	de/report/de_significant_genes_heatmap.txt
de_report_most_differential_genes_tables	true:report_plot:optional	de/report/de_most_differential_genes_tables.txt
de_report_most_differential_genes_boxplots	true:report_plot:optional	de/report/de_most_differential_genes_boxplots.txt
de_report_oras	true:report_title:ora	Over Representation Analysis
de_report_ora_enriched_gene_sets_summary	true:report_plot:ora	de/report/de_ora_enriched_gene_sets_summary.txt
de_report_ora_enriched_gene_sets_barcharts	false:report_plot:ora	de/report/de_ora_enriched_gene_sets_barcharts.txt
de_report_ora_enriched_gene_sets_ridgeplot	false:report_plot:ora	de/report/de_ora_enriched_gene_sets_ridgeplot.txt
de_report_ora_enriched_gene_sets_boxplots	true:report_plot:ora	de/report/de_ora_enriched_gene_sets_boxplots.txt
de_report_ora_enriched_gene_sets_network_plots	true:report_plot:ora	de/report/de_ora_enriched_gene_sets_network_plots.txt
de_report_ora_underenriched_gene_barcharts	true:report_plot:ora	de/report/de_ora_underenriched_gene_sets_barcharts.txt
de_report_upstream_regulators	true:report_title:ura	Upstream Regulators
de_report_ura_summary	true:report_plot:ura	de/report/de_ura_summary.txt
de_report_ura_barcharts	false:report_plot:ura	de/report/de_ura_barcharts.txt
de_report_ura_ridgeplot	false:report_plot:ura	de/report/de_ura_ridgeplot.txt
de_report_ura_boxplots	true:report_plot:ura	de/report/de_ura_boxplots.txt
de_report_ura_network_plots	true:report_plot:ura	de/report/de_ura_network_plots.txt
de_report_spatial_enrichment	true:report_title:spatial	Spatial Analysis
de_report_spatial_enrichment_table	true:report_plot:spatial	de/report/de_spatial_enrichment_table.txt
de_report_spatial_enrichment_distribution_plots	true:report_plot:spatial	de/report/de_spatial_enrichment_distribution_plots.txt
de_report_methodology	true:report_title:optional	Methodology
de_report_core_workflow_methods	true:report_text:optional	methods/de/core_workflow.txt
de_report_spatial_analysis_methods	true:report_text:optional	methods/de/spatial_analysis.txt
de_report_over_representation_analysis_methods	true:report_text:ora	methods/de/over_representation_analysis.txt
de_report_upstream_regulators_methods	true:report_text:ura	methods/de/upstream_regulator_analysis.txt
de_report_extras	true:report_title:optional	Extras
de_report_citation	true:report_text:optional	citation.txt
de_end_report	true:report_core:core	none

##---- mde ----##

mde_sub_directories_core	true:core:directory	none

mde_file_all_genes_IDs	true:core:file	none
mde_file_genes_significant_in_any_comparison_IDs	true:core:file	none
mde_file_genes_significant_in_all_comparisons_IDs	true:core:file	none
mde_file_all_genes_symbols	true:core:file	none
mde_file_genes_significant_in_any_comparison_symbols	true:core:file	none
mde_file_genes_significant_in_all_comparisons_symbols	true:core:file	none
mde_file_all_genes_annotated	true:core:file	none
mde_file_genes_significant_in_any_comparison_annotated	true:core:file	none
mde_file_genes_significant_in_all_comparisons_annotated	true:core:file	none

mde_analysis_pairwise_overlap	true:statistical:pairwise_overlap	none
mde_differential_expression_signature	true:statistical:differential_expression_signature	none

mde_start_plots	true:plot_core:core	none
mde_plot_distribution_of_expression_values	true:plot:optional	mde/plots/mde_distribution_of_expression_values.txt
mde_plot_PCA_contribution_of_components	true:plot:optional	mde/plots/mde_PCA_contributions_of_components.txt
mde_plot_PCA_scatterplot	true:plot:optional	mde/plots/mde_PCA_scatterplot.txt
mde_plot_correlation_analysis_heatmap	true:plot:optional	mde/plots/mde_correlation_analysis_heatmap.txt
mde_plot_most_expressed_genes_tables	false:plot:optional	mde/plots/mde_most_expressed_genes_tables.txt
mde_plot_most_expressed_genes_boxplots	false:plot:optional	mde/plots/mde_most_expressed_genes_boxplots.txt
mde_plot_number_of_significant_genes	true:plot:optional	mde/plots/mde_number_of_significant_genes.txt
mde_plot_significant_genes_heatmap	true:plot:optional	mde/plots/mde_significant_genes_heatmap.txt
mde_plot_pairwise_overlap_table	true:plot:optional	mde/plots/mde_pairwise_overlap_table.txt
mde_plot_fold_vs_fold_scatterplot	true:plot:optional	mde/plots/mde_fold_vs_fold_scatterplots.txt
mde_plot_differential_expression_signatures_metagene_boxplots	true:plot:optional	mde/plots/mde_differential_expression_signature_metagene_boxplots.txt
mde_plot_differential_expression_signatures_heatmap	true:plot:optional	mde/plots/mde_differential_expression_signatures_heatmap.txt
mde_plot_differential_expression_signatures_ora_barcharts	true:plot:ora	mde/plots/mde_differential_expression_signatures_ora_barchart.txt
mde_plot_differential_expression_signatures_ora_boxplots	true:plot:ora	mde/plots/mde_differential_expression_signatures_ora_boxplots.txt
mde_plot_differential_expression_signatures_ora_network_plots	true:plot:ora	mde/plots/mde_differential_expression_signatures_ora_network_plots.txt

mde_end_plots	true:plot_core:core	none
mde_run_r	true:plot_core:core	none

mde_start_report	true:report_core:core	none
mde_report_expression	true:report_title:optional	Expression
mde_report_distribution_of_expression_values	true:report_plot:optional	mde/report/mde_distribution_of_expression_values.txt
mde_report_PCA_contribution_of_components	true:report_plot:optional	mde/report/mde_PCA_contributions_of_components.txt
mde_report_PCA_scatterplot	true:report_plot:optional	mde/report/mde_PCA_scatterplot.txt
mde_report_correlation_analysis_heatmap	true:report_plot:optional	mde/report/mde_correlation_analysis_heatmap.txt
mde_report_most_expressed_genes_tables	false:report_plot:optional	mde/report/mde_most_expressed_genes_tables.txt
mde_report_most_expressed_genes_boxplots	false:report_plot:optional	mde/report/mde_most_expressed_genes_boxplots.txt
mde_report_multiple_differential_expression	true:report_title:optional	Multiple Differential Expression
mde_report_number_of_significant_genes	true:report_plot:optional	mde/report/mde_number_of_significant_genes.txt
mde_report_significant_genes_heatmap	true:report_plot:optional	mde/report/mde_significant_genes_heatmap.txt
mde_report_pairwise_overlap_table	true:report_plot:optional	mde/report/mde_pairwise_overlap_table.txt
mde_report_fold_vs_fold_scatterplot	true:report_plot:optional	mde/report/mde_fold_vs_fold_scatterplots.txt
mde_report_differential_expression_signatures	true:report_title:optional	Differential Expression Signatures
mde_report_differential_expression_signatures_meta_plus_heatmap	true:report_plot:optional	mde/report/mde_differential_expression_signatures_meta_plus_heatmap.txt
mde_report_differential_expression_signatures_metagene_boxplots	false:report_plot:optional	mde/report/mde_differential_expression_signatures_metagene_boxplots.txt
mde_report_differential_expression_signatures_heatmap	false:report_plot:optional	mde/report/mde_differential_expression_signatures_heatmap.txt
mde_report_differential_expression_signatures_ora_barcharts	true:report_plot:ora	mde/report/mde_differential_expression_signatures_ora_barchart.txt
mde_report_differential_expression_signatures_ora_boxplots	true:report_plot:ora	mde/report/mde_differential_expression_signatures_ora_boxplots.txt
mde_report_differential_expression_signatures_ora_network_plots	true:report_plot:ora	mde/report/mde_differential_expression_signatures_ora_network_plots.txt

mde_report_methodology	true:report_title:optional	Methodology
mde_report_core_workflow_methods	true:report_text:optional	methods/mde/core_workflow.txt
mde_report_differential_expression_signatures_methods	true:report_text:optional	methods/mde/differential_expression_signatures.txt
mde_report_over_representation_analysis_methods	true:report_text:ora	methods/mde/over_representation_analysis.txt
mde_report_extras	true:report_title:optional	Extras
mde_report_citation	true:report_text:optional	citation.txt
mde_end_report	true:report_core:core	none
