Index

A

add_volcano_plot() (in module magine.plotting.volcano_plots)

all_genes_from_df() (magine.enrichment.enrichment_result.EnrichmentResult method)

B

BaseData (class in magine.data.base)

build_network() (in module magine.networks.network_generator) by_sample (magine.data.experimental_data.Sample property)

C

calc_dist() (magine.enrichment.enrichment_result.EnrichmentResult method) check_synonym_dict() (magine.mappings.ChemicalMapper method) (magine.mappings.GeneMapper method) chem_name_to_hmdb (magine.mappings.ChemicalMapper property) ChemicalMapper (class in magine.mappings) clean_drug_pert_geo() (in module magine.enrichment.enrichr) clean_lincs() (in module magine.enrichment.enrichr) clean_term_names() (in module magine.enrichment.enrichr) clean_tf_names() (in module magine.enrichment.enrichr)

cluster_distance_mat() (in module magine.plotting.heatmaps) compounds (magine.data.experimental_data.ExperimentalData property) convert_kegg_nodes() (magine.mappings.ChemicalMapper method) (magine.mappings.GeneMapper method) create_background_network() (in module magine.networks.network_generator) create_mask() (in module magine.plotting.volcano_plots) create_summary_table() (magine.data.experimental_data.ExperimentalData method) create_venn2() (in module magine.plotting.venn_diagram_maker) create_venn3() (in module magine.plotting.venn_diagram_maker) create_yadf_filters() (in module magine.html_templates.html_tools)

D

dist_matrix() (magine.enrichment.enrichment_result.EnrichmentResult method) down (magine.data.experimental_data.Sample property) down_by_sample (magine.data.experimental_data.Sample property) download_biogrid() (in module magine.networks.databases)

download_db() (magine.mappings.databases.HMDB method) download_reactome_fi() (in module magine.networks.databases) download_signor() (in module magine.networks.databases) drugbank_to_hmdb (magine.mappings.ChemicalMapper property)

E

EnrichmentResult (class in magine.enrichment.enrichment_result) Enrichr (class in magine.enrichment.enrichr) exp_methods (magine.data.experimental_data.ExperimentalData property) (magine.data.experimental_data.Sample property)

expand_by_db() (in module magine.networks.network_generator) ExperimentalData (class in magine.data.experimental_data)

F

filter_based_on_words() (magine.enrichment.enrichment_result.EnrichmentResult method) filter_multi() (magine.enrichment.enrichment_result.EnrichmentResult method)

filter_rows() (magine.enrichment.enrichment_result.EnrichmentResult method) find_similar_terms() (magine.enrichment.enrichment_result.EnrichmentResult method) format_ploty() (in module magine.html_templates.html_tools)

G

gene_name_to_alias_name (magine.mappings.GeneMapper property) gene_name_to_ensembl (magine.mappings.GeneMapper property) gene_name_to_kegg (magine.mappings.GeneMapper property) gene_name_to_uniprot (magine.mappings.GeneMapper property)

GeneMapper (class in magine.mappings) genes (magine.data.experimental_data.ExperimentalData property) get_background_list() (in module magine.enrichment.enrichr) get_measured_by_datatype() (magine.data.experimental_data.ExperimentalData method)

H

heatmap() (magine.data.base.BaseData method) heatmap_by_terms() (in module magine.plotting.heatmaps) heatmap_from_array() (in module magine.plotting.heatmaps) HMDB (class in magine.mappings.databases)

hmdb_accession_to_main (magine.mappings.ChemicalMapper property) hmdb_main_to_protein (magine.mappings.ChemicalMapper property) hmdb_to_kegg (magine.mappings.ChemicalMapper property) hmdb_to_protein (magine.mappings.ChemicalMapper property)

I

id_list (magine.data.experimental_data.Sample property)

K

kegg_to_gene_name (magine.mappings.GeneMapper property) kegg_to_hugo() (magine.mappings.GeneMapper method)

kegg_to_symbol_through_uniprot() (magine.mappings.GeneMapper method) kegg_to_uniprot (magine.mappings.GeneMapper property)

L

label_list (magine.data.experimental_data.Sample property) load_biogrid_network() (in module magine.networks.databases) load_db() (magine.mappings.databases.HMDB method) load_enrichment_csv() (in module magine.enrichment.enrichment_result) load_hgnc() (in module magine.mappings.databases) load_hmdb_network() (in module magine.networks.databases)

load_kegg() (in module magine.networks.databases) load_kegg_mappings() (in module magine.networks.databases) load_ncbi() (in module magine.mappings.databases) load_reactome_fi() (in module magine.networks.databases) load_signor() (in module magine.networks.databases) load_uniprot() (in module magine.mappings.databases) log2_normalize_df() (magine.data.base.BaseData method)

M

magine.html_templates.html_tools module magine.mappings module magine.mappings.databases module magine.networks.databases module magine.networks.network_generator module magine.plotting.heatmaps module magine.plotting.species_plotting module

magine.plotting.venn_diagram_maker module magine.plotting.volcano_plots module module magine.html_templates.html_tools magine.mappings magine.mappings.databases magine.networks.databases magine.networks.network_generator magine.plotting.heatmaps magine.plotting.species_plotting magine.plotting.venn_diagram_maker magine.plotting.volcano_plots

N

ncbi_to_symbol (magine.mappings.GeneMapper property)

P

pivoter() (magine.data.base.BaseData method) plot_all() (magine.data.experimental_data.Sample method) plot_dataframe() (in module magine.plotting.species_plotting) plot_genes_by_ont() (in module magine.plotting.species_plotting) plot_histogram() (magine.data.experimental_data.Sample method) plot_pie_sig_ratio() (magine.data.experimental_data.Sample method)

plot_species() (in module magine.plotting.species_plotting) (magine.data.experimental_data.Sample method) present_in_all_columns() (magine.data.base.BaseData method) print_info() (magine.mappings.ChemicalMapper method) print_valid_libs() (magine.enrichment.enrichr.Enrichr method) proteins (magine.data.experimental_data.ExperimentalData property)

R

remove_redundant() (magine.enrichment.enrichment_result.EnrichmentResult method) require_n_sig() (magine.data.base.BaseData method) rna (magine.data.experimental_data.ExperimentalData property)

run() (magine.enrichment.enrichr.Enrichr method) run_enrichment_for_project() (in module magine.enrichment.enrichr) run_samples() (magine.enrichment.enrichr.Enrichr method)

S

Sample (class in magine.data.experimental_data) sample_ids (magine.data.experimental_data.ExperimentalData property) (magine.data.experimental_data.Sample property) save_plot() (in module magine.plotting.volcano_plots)

show_terms_below() (magine.enrichment.enrichment_result.EnrichmentResult method) sig (magine.data.base.BaseData property) species (magine.data.experimental_data.ExperimentalData property) subset() (magine.data.experimental_data.ExperimentalData method) (magine.data.experimental_data.Sample method)

T

term_to_genes() (magine.enrichment.enrichment_result.EnrichmentResult method)

term_to_genes_dict() (magine.enrichment.enrichment_result.EnrichmentResult method)

U

uniprot_to_gene_name (magine.mappings.GeneMapper property) uniprot_to_kegg (magine.mappings.GeneMapper property)

unique_terms() (magine.enrichment.enrichment_result.EnrichmentResult method) up (magine.data.experimental_data.Sample property) up_by_sample (magine.data.experimental_data.Sample property)

V

valid_columns (magine.mappings.ChemicalMapper attribute) volcano_analysis() (magine.data.experimental_data.ExperimentalData method)

volcano_by_sample() (magine.data.experimental_data.Sample method) volcano_plot() (in module magine.plotting.volcano_plots) (magine.data.experimental_data.Sample method)

W

write_filter_table() (in module magine.html_templates.html_tools)

write_table_to_html() (in module magine.plotting.species_plotting)