Index

_

_abc_impl (modalysis.server.models.DmrAnnotateRequest attribute) (modalysis.server.models.DmrCommonGenesRequest attribute) (modalysis.server.models.DmrFormatRequest attribute) (modalysis.server.models.DmrGeneCountsRequest attribute) (modalysis.server.models.GffAnnotateRequest attribute) (modalysis.server.models.GffFormatRequest attribute) (modalysis.server.models.PileupFormatRequest attribute) (modalysis.server.models.PileupMergeRequest attribute) (modalysis.server.models.PlotCommonGenesVennRequest attribute) (modalysis.server.models.PlotDmrDotplotRequest attribute) (modalysis.server.models.PlotGeneHeatmapRequest attribute) (modalysis.server.models.PlotMeanMethylationRequest attribute) _accumulate_pileup() (in module modalysis.core.plots.mean_methylation)

_accumulate_pileup_per_gene() (in module modalysis.core.plots.gene_heatmap) _build_gene_coordinate_lookup() (in module modalysis.core.plots.dmr_dotplot) _collect_dmr_positions() (in module modalysis.core.plots.dmr_dotplot) _collect_genes_by_combination() (in module modalysis.core.plots.gene_heatmap) _collect_negative_gene_sets() (in module modalysis.core.plots.common_genes_venn) _draw_venn_panel() (in module modalysis.core.plots.common_genes_venn) _excel_inline_string_cell() (in module modalysis.core.dmr) _excel_number_cell() (in module modalysis.core.dmr) _find_consensus_window() (in module modalysis.core.plots.dmr_dotplot) _find_overlapping_regions() (in module modalysis.core.plots.mean_methylation) _render_dotplot() (in module modalysis.core.plots.dmr_dotplot) _to_excel_column_name() (in module modalysis.core.dmr) _write_gene_counts_excel() (in module modalysis.core.dmr)

A

allowed_chromosomes (modalysis.server.models.DmrFormatRequest attribute) (modalysis.server.models.GffFormatRequest attribute) (modalysis.server.models.PileupFormatRequest attribute) annotate() (in module modalysis.core.dmr) (in module modalysis.core.gff) annotated_dmr_paths (modalysis.server.models.DmrCommonGenesRequest attribute) (modalysis.server.models.DmrGeneCountsRequest attribute) (modalysis.server.models.PlotCommonGenesVennRequest attribute) (modalysis.server.models.PlotDmrDotplotRequest attribute) (modalysis.server.models.PlotGeneHeatmapRequest attribute)

annotated_gff_path (modalysis.server.models.DmrCommonGenesRequest attribute) (modalysis.server.models.DmrGeneCountsRequest attribute) (modalysis.server.models.PlotDmrDotplotRequest attribute) (modalysis.server.models.PlotGeneHeatmapRequest attribute)

B

body (modalysis.core.gene_regions.ChromosomeRegions attribute) body_starts (modalysis.core.gene_regions.ChromosomeRegions attribute)

build_gene_regions() (in module modalysis.core.gene_regions) build_parser() (in module modalysis.cli.parsers)

C

chromosome_order (modalysis.server.models.PlotMeanMethylationRequest attribute)

ChromosomeRegions (class in modalysis.core.gene_regions) common_genes() (in module modalysis.core.dmr)

D

dmr_annotate() (in module modalysis.client.dmr) (in module modalysis.server.dmr) dmr_common_genes() (in module modalysis.client.dmr) (in module modalysis.server.dmr) dmr_format() (in module modalysis.client.dmr) (in module modalysis.server.dmr)

dmr_gene_counts() (in module modalysis.client.dmr) (in module modalysis.server.dmr) dmr_path (modalysis.server.models.DmrAnnotateRequest attribute) DmrAnnotateRequest (class in modalysis.server.models) DmrCommonGenesRequest (class in modalysis.server.models) DmrFormatRequest (class in modalysis.server.models) DmrGeneCountsRequest (class in modalysis.server.models)

E

effect_signs (modalysis.server.models.PlotDmrDotplotRequest attribute) (modalysis.server.models.PlotGeneHeatmapRequest attribute) enhancer (modalysis.core.gene_regions.ChromosomeRegions attribute) enhancer_starts (modalysis.core.gene_regions.ChromosomeRegions attribute) expression_labels (modalysis.server.models.DmrCommonGenesRequest attribute) (modalysis.server.models.DmrGeneCountsRequest attribute) (modalysis.server.models.GffAnnotateRequest attribute) (modalysis.server.models.PlotDmrDotplotRequest attribute) (modalysis.server.models.PlotGeneHeatmapRequest attribute)

expression_paths (modalysis.server.models.GffAnnotateRequest attribute)

F

find_genes_at_position() (in module modalysis.core.gene_regions) find_genes_overlapping_interval() (in module modalysis.core.gene_regions) format() (in module modalysis.core.dmr) (in module modalysis.core.gff) (in module modalysis.core.pileup)

format_modification_label() (in module modalysis.core.plots.label_format)

G

gene_counts() (in module modalysis.core.dmr) gff_annotate() (in module modalysis.client.gff) (in module modalysis.server.gff) gff_format() (in module modalysis.client.gff) (in module modalysis.server.gff) gff_path (modalysis.server.models.DmrAnnotateRequest attribute) (modalysis.server.models.GffAnnotateRequest attribute) (modalysis.server.models.PlotDmrDotplotRequest attribute) (modalysis.server.models.PlotGeneHeatmapRequest attribute) (modalysis.server.models.PlotMeanMethylationRequest attribute)

GffAnnotateRequest (class in modalysis.server.models) GffFormatRequest (class in modalysis.server.models)

H

handle_dmr_annotate() (in module modalysis.cli.handlers.dmr) handle_dmr_common_genes() (in module modalysis.cli.handlers.dmr) handle_dmr_format() (in module modalysis.cli.handlers.dmr) handle_dmr_gene_counts() (in module modalysis.cli.handlers.dmr) handle_gff_annotate() (in module modalysis.cli.handlers.gff) handle_gff_format() (in module modalysis.cli.handlers.gff)

handle_pileup_format() (in module modalysis.cli.handlers.pileup) handle_pileup_merge() (in module modalysis.cli.handlers.pileup) handle_plot_common_genes_venn() (in module modalysis.cli.handlers.plot) handle_plot_dmr_dotplot() (in module modalysis.cli.handlers.plot) handle_plot_gene_heatmap() (in module modalysis.cli.handlers.plot) handle_plot_mean_methylation() (in module modalysis.cli.handlers.plot) handle_server() (in module modalysis.cli.handlers.server)

I

input_path (modalysis.server.models.DmrFormatRequest attribute) (modalysis.server.models.GffFormatRequest attribute) (modalysis.server.models.PileupFormatRequest attribute)

L

labels (modalysis.server.models.PlotMeanMethylationRequest attribute)

lifespan() (in module modalysis.server.main)

M

main() (in module modalysis) manifestation_labels (modalysis.server.models.DmrCommonGenesRequest attribute) (modalysis.server.models.DmrGeneCountsRequest attribute) (modalysis.server.models.PlotDmrDotplotRequest attribute) (modalysis.server.models.PlotGeneHeatmapRequest attribute) manifestations (modalysis.server.models.DmrCommonGenesRequest attribute) (modalysis.server.models.DmrGeneCountsRequest attribute) (modalysis.server.models.PlotCommonGenesVennRequest attribute) (modalysis.server.models.PlotDmrDotplotRequest attribute) (modalysis.server.models.PlotGeneHeatmapRequest attribute) max_p_value (modalysis.server.models.DmrFormatRequest attribute) merge() (in module modalysis.core.pileup) merged_pileup_paths (modalysis.server.models.PlotGeneHeatmapRequest attribute) (modalysis.server.models.PlotMeanMethylationRequest attribute) min_file_coverage (modalysis.server.models.PileupMergeRequest attribute) min_files (modalysis.server.models.PileupMergeRequest attribute) min_pct_a_samples (modalysis.server.models.DmrFormatRequest attribute) min_pct_b_samples (modalysis.server.models.DmrFormatRequest attribute) min_reads (modalysis.server.models.DmrFormatRequest attribute) (modalysis.server.models.PileupMergeRequest attribute) min_score (modalysis.server.models.DmrFormatRequest attribute) modalysis module modalysis.cli.handlers.dmr module modalysis.cli.handlers.gff module modalysis.cli.handlers.pileup module modalysis.cli.handlers.plot module modalysis.cli.handlers.server module modalysis.cli.parsers module modalysis.cli.parsers.dmr module modalysis.cli.parsers.gff module modalysis.cli.parsers.pileup module modalysis.cli.parsers.plot module modalysis.cli.parsers.server module modalysis.client.dmr module modalysis.client.gff module modalysis.client.pileup module modalysis.client.plot module modalysis.core.chromosomes module modalysis.core.dmr module modalysis.core.expression module modalysis.core.gene_regions module modalysis.core.gff module modalysis.core.pileup module modalysis.core.plots.common_genes_venn module modalysis.core.plots.dmr_dotplot module modalysis.core.plots.gene_heatmap module

modalysis.core.plots.label_format module modalysis.core.plots.mean_methylation module modalysis.server.dmr module modalysis.server.gff module modalysis.server.main module modalysis.server.models module modalysis.server.pileup module modalysis.server.plot module model_config (modalysis.server.models.DmrAnnotateRequest attribute) (modalysis.server.models.DmrCommonGenesRequest attribute) (modalysis.server.models.DmrFormatRequest attribute) (modalysis.server.models.DmrGeneCountsRequest attribute) (modalysis.server.models.GffAnnotateRequest attribute) (modalysis.server.models.GffFormatRequest attribute) (modalysis.server.models.PileupFormatRequest attribute) (modalysis.server.models.PileupMergeRequest attribute) (modalysis.server.models.PlotCommonGenesVennRequest attribute) (modalysis.server.models.PlotDmrDotplotRequest attribute) (modalysis.server.models.PlotGeneHeatmapRequest attribute) (modalysis.server.models.PlotMeanMethylationRequest attribute) modification_a (modalysis.server.models.DmrCommonGenesRequest attribute) (modalysis.server.models.PlotCommonGenesVennRequest attribute) modification_b (modalysis.server.models.DmrCommonGenesRequest attribute) (modalysis.server.models.PlotCommonGenesVennRequest attribute) modifications (modalysis.server.models.DmrCommonGenesRequest attribute) (modalysis.server.models.DmrGeneCountsRequest attribute) (modalysis.server.models.PlotCommonGenesVennRequest attribute) (modalysis.server.models.PlotDmrDotplotRequest attribute) (modalysis.server.models.PlotGeneHeatmapRequest attribute) module modalysis modalysis.cli.handlers.dmr modalysis.cli.handlers.gff modalysis.cli.handlers.pileup modalysis.cli.handlers.plot modalysis.cli.handlers.server modalysis.cli.parsers modalysis.cli.parsers.dmr modalysis.cli.parsers.gff modalysis.cli.parsers.pileup modalysis.cli.parsers.plot modalysis.cli.parsers.server modalysis.client.dmr modalysis.client.gff modalysis.client.pileup modalysis.client.plot modalysis.core.chromosomes modalysis.core.dmr modalysis.core.expression modalysis.core.gene_regions modalysis.core.gff modalysis.core.pileup modalysis.core.plots.common_genes_venn modalysis.core.plots.dmr_dotplot modalysis.core.plots.gene_heatmap modalysis.core.plots.label_format modalysis.core.plots.mean_methylation modalysis.server.dmr modalysis.server.gff modalysis.server.main modalysis.server.models modalysis.server.pileup modalysis.server.plot

N

normalize_allowed_chromosomes() (in module modalysis.core.chromosomes)

O

output_excel (modalysis.server.models.DmrGeneCountsRequest attribute) output_name (modalysis.server.models.DmrAnnotateRequest attribute) (modalysis.server.models.DmrCommonGenesRequest attribute) (modalysis.server.models.DmrFormatRequest attribute) (modalysis.server.models.DmrGeneCountsRequest attribute) (modalysis.server.models.GffAnnotateRequest attribute) (modalysis.server.models.GffFormatRequest attribute) (modalysis.server.models.PileupFormatRequest attribute) (modalysis.server.models.PileupMergeRequest attribute) (modalysis.server.models.PlotCommonGenesVennRequest attribute) (modalysis.server.models.PlotDmrDotplotRequest attribute) (modalysis.server.models.PlotGeneHeatmapRequest attribute) (modalysis.server.models.PlotMeanMethylationRequest attribute)

output_path (modalysis.server.models.DmrAnnotateRequest attribute) (modalysis.server.models.DmrCommonGenesRequest attribute) (modalysis.server.models.DmrFormatRequest attribute) (modalysis.server.models.DmrGeneCountsRequest attribute) (modalysis.server.models.GffAnnotateRequest attribute) (modalysis.server.models.GffFormatRequest attribute) (modalysis.server.models.PileupFormatRequest attribute) (modalysis.server.models.PileupMergeRequest attribute) (modalysis.server.models.PlotCommonGenesVennRequest attribute) (modalysis.server.models.PlotDmrDotplotRequest attribute) (modalysis.server.models.PlotGeneHeatmapRequest attribute) (modalysis.server.models.PlotMeanMethylationRequest attribute)

P

parse_expression_field() (in module modalysis.core.expression) parse_gff() (in module modalysis.core.gene_regions) pileup_format() (in module modalysis.client.pileup) (in module modalysis.server.pileup) pileup_manifestations (modalysis.server.models.PlotGeneHeatmapRequest attribute) pileup_merge() (in module modalysis.client.pileup) (in module modalysis.server.pileup) pileup_modifications (modalysis.server.models.PlotGeneHeatmapRequest attribute) pileup_paths (modalysis.server.models.PileupMergeRequest attribute) PileupFormatRequest (class in modalysis.server.models) PileupMergeRequest (class in modalysis.server.models) plot_common_genes_venn() (in module modalysis.client.plot) (in module modalysis.core.plots.common_genes_venn) (in module modalysis.server.plot) plot_dmr_dotplot() (in module modalysis.client.plot) (in module modalysis.core.plots.dmr_dotplot) (in module modalysis.server.plot)

plot_gene_heatmap() (in module modalysis.client.plot) (in module modalysis.core.plots.gene_heatmap) (in module modalysis.server.plot) plot_mean_methylation() (in module modalysis.client.plot) (in module modalysis.core.plots.mean_methylation) (in module modalysis.server.plot) plot_title (modalysis.server.models.PlotMeanMethylationRequest attribute) PlotCommonGenesVennRequest (class in modalysis.server.models) PlotDmrDotplotRequest (class in modalysis.server.models) PlotGeneHeatmapRequest (class in modalysis.server.models) PlotMeanMethylationRequest (class in modalysis.server.models) promoter (modalysis.core.gene_regions.ChromosomeRegions attribute) promoter_starts (modalysis.core.gene_regions.ChromosomeRegions attribute)

R

register_dmr_parser() (in module modalysis.cli.parsers.dmr) register_gff_parser() (in module modalysis.cli.parsers.gff)

register_pileup_parser() (in module modalysis.cli.parsers.pileup) register_plot_parser() (in module modalysis.cli.parsers.plot) register_server_parser() (in module modalysis.cli.parsers.server)

S

show_gene_labels (modalysis.server.models.PlotDmrDotplotRequest attribute) (modalysis.server.models.PlotGeneHeatmapRequest attribute)

Y

y_max (modalysis.server.models.PlotMeanMethylationRequest attribute)

y_min (modalysis.server.models.PlotMeanMethylationRequest attribute)