magine
0.1a1
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MAGINE Modules Reference
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Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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L
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M
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P
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R
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S
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T
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U
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V
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W
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)
by_sample (magine.data.experimental_data.Sample property)
C
calc_dist() (magine.enrichment.enrichment_result.EnrichmentResult method)
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)
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)
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)
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
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)
I
id_list (magine.data.experimental_data.Sample property)
L
label_list (magine.data.experimental_data.Sample property)
load_enrichment_csv() (in module magine.enrichment.enrichment_result)
log2_normalize_df() (magine.data.base.BaseData method)
M
magine.html_templates.html_tools
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.plotting.heatmaps
magine.plotting.species_plotting
magine.plotting.venn_diagram_maker
magine.plotting.volcano_plots
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_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
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
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)