Index

Symbols

--add cli-explain command line option cli-run command line option --debug cli-explain command line option cli-orchestrate command line option cli-run command line option cli-stability command line option --gene cli-plot command line option --mode cli-stability command line option --n-cpus cli-explain command line option cli-run command line option cli-stability command line option --n-gpus cli-explain command line option cli-run command line option cli-stability command line option --n-iters cli-explain command line option cli-run command line option cli-stability command line option

--no-add cli-explain command line option cli-run command line option --no-debug cli-explain command line option cli-orchestrate command line option cli-run command line option cli-stability command line option --no-verbosity cli-explain command line option cli-orchestrate command line option cli-run command line option cli-stability command line option --verbosity cli-explain command line option cli-orchestrate command line option cli-run command line option cli-stability command line option --version cli command line option cli-explain command line option cli-orchestrate command line option cli-plot command line option cli-run command line option cli-stability command line option

A

alpha (drexml.pystab.NogueiraTest attribute)

B

build_circuits_fname() (in module drexml.utils) build_gene_exp_fname() (in module drexml.utils)

build_genes_fname() (in module drexml.utils) build_pathvals_fname() (in module drexml.utils) build_stability_dict() (in module drexml.explain)

C

check_cli_arg_is_bool() (in module drexml.utils) check_gputree_availability() (in module drexml.utils) cli command line option --version cli-explain command line option --add --debug --n-cpus --n-gpus --n-iters --no-add --no-debug --no-verbosity --verbosity --version DISEASE_PATH cli-orchestrate command line option --debug --no-debug --no-verbosity --verbosity --version DISEASE_PATH cli-plot command line option --gene --version OUTPUT_FOLDER SCORE_PATH SEL_PATH STABILITY_PATH

cli-run command line option --add --debug --n-cpus --n-gpus --n-iters --no-add --no-debug --no-verbosity --verbosity --version DISEASE_PATH cli-stability command line option --debug --mode --n-cpus --n-gpus --n-iters --no-debug --no-verbosity --verbosity --version DISEASE_PATH compute_corr_sign() (in module drexml.explain) compute_shap_fs() (in module drexml.explain) compute_shap_relevance() (in module drexml.explain) compute_shap_values_() (in module drexml.explain) convert_names() (in module drexml.utils)

D

DISEASE_PATH cli-explain command line option cli-orchestrate command line option cli-run command line option cli-stability command line option drexml.datasets module drexml.explain module

drexml.models module drexml.plotting module drexml.pystab module drexml.utils module

E

ensure_zenodo() (in module drexml.utils) error (drexml.pystab.NogueiraTest attribute)

estimator (drexml.pystab.NogueiraTest attribute) extract_estimator() (in module drexml.models)

F

fdr() (in module drexml.pystab)

fetch_file() (in module drexml.datasets) filter_scores() (drexml.plotting.RepurposingResult method)

G

get_cuda_lib() (in module drexml.utils) get_cuda_version() (in module drexml.utils) get_data() (in module drexml.datasets) get_disease_data() (in module drexml.datasets) get_gda() (in module drexml.datasets) get_index_name_options() (in module drexml.datasets) get_latest_record() (in module drexml.utils) get_model() (in module drexml.models)

get_number_cuda_devices() (in module drexml.utils) get_number_cuda_devices_() (in module drexml.utils) get_out_path() (in module drexml.utils) get_quantile_by_circuit() (in module drexml.explain) get_resource_path() (in module drexml.utils) get_rf_space() (in module drexml.models) get_stab() (in module drexml.utils) get_stable_circuits() (drexml.plotting.RepurposingResult method) get_version() (in module drexml.utils)

L

load_atc() (in module drexml.datasets) load_df() (in module drexml.datasets) load_disgenet() (in module drexml.datasets)

load_drugbank() (in module drexml.datasets) load_physiological_circuits() (in module drexml.datasets) lower (drexml.pystab.NogueiraTest attribute)

M

matcorr() (in module drexml.explain) module drexml.datasets drexml.explain drexml.models drexml.plotting drexml.pystab drexml.utils

N

NogueiraTest (class in drexml.pystab)

nogueria_test() (in module drexml.pystab)

O

OUTPUT_FOLDER cli-plot command line option

P

parse_stab() (in module drexml.utils) plot_gene_profile() (drexml.plotting.RepurposingResult method) plot_metrics() (drexml.plotting.RepurposingResult method) plot_relevance_heatmap() (drexml.plotting.RepurposingResult method)

preprocess_activities() (in module drexml.datasets) preprocess_frame() (in module drexml.datasets) preprocess_genes() (in module drexml.datasets) preprocess_gexp() (in module drexml.datasets) preprocess_map() (in module drexml.datasets)

R

read_activity_normalizer() (in module drexml.utils) read_circuits_column() (in module drexml.utils) read_disease_config() (in module drexml.utils) read_disease_id() (in module drexml.utils)

read_path_based() (in module drexml.utils) read_seed_genes() (in module drexml.utils) read_use_physio() (in module drexml.utils) read_version_based() (in module drexml.utils) RepurposingResult (class in drexml.plotting)

S

score_mat (drexml.plotting.RepurposingResult attribute) SCORE_PATH cli-plot command line option sel_mat (drexml.plotting.RepurposingResult attribute)

SEL_PATH cli-plot command line option stab_mat (drexml.plotting.RepurposingResult attribute) STABILITY_PATH cli-plot command line option

U

update_circuits() (in module drexml.utils) update_gene_exp() (in module drexml.utils)

update_genes() (in module drexml.utils) update_pathvals() (in module drexml.utils) upper (drexml.pystab.NogueiraTest attribute)

V

var (drexml.pystab.NogueiraTest attribute)