Index

Symbols

--chain-pca pathway_forte-prediction-subtype command line option --explained-variance <explained_variance> pathway_forte-prediction-subtype command line option --inner-cv <inner_cv> pathway_forte-prediction-binary command line option pathway_forte-prediction-subtype command line option pathway_forte-prediction-survival command line option pathway_forte-prediction-test-stability-prediction command line option --no-threshold pathway_forte-ora-hypergeometric command line option --outer-cv <outer_cv> pathway_forte-prediction-binary command line option pathway_forte-prediction-subtype command line option pathway_forte-prediction-survival command line option pathway_forte-prediction-test-stability-prediction command line option --turn-off-warnings pathway_forte-prediction-binary command line option pathway_forte-prediction-subtype command line option pathway_forte-prediction-survival command line option pathway_forte-prediction-test-stability-prediction command line option -d, --data <data> pathway_forte-fcs-gsea command line option pathway_forte-fcs-gsea-msig command line option pathway_forte-fcs-ssgsea command line option pathway_forte-prediction-binary command line option pathway_forte-prediction-survival command line option

-d, --genesets <genesets> pathway_forte-ora-hypergeometric command line option -d, --ssgsea <ssgsea> pathway_forte-prediction-subtype command line option -i, --max_iterations <max_iterations> pathway_forte-prediction-binary command line option pathway_forte-prediction-test-stability-prediction command line option -o, --output <output> pathway_forte-ora-hypergeometric command line option -p, --permutations <permutations> pathway_forte-fcs-gsea command line option -p, --phenotypes-path <phenotypes_path> pathway_forte-prediction-test-stability-prediction command line option -s, --fold-changes <fold_changes> pathway_forte-ora-hypergeometric command line option -s, --ssgsea-scores-path <ssgsea_scores_path> pathway_forte-prediction-test-stability-prediction command line option -s, --subtypes <subtypes> pathway_forte-prediction-subtype command line option

B

binary (in module pathway_forte.prediction)

BIO2BEL_DATA_DIR (in module pathway_forte.constants)

C

check_gmt_files() (in module pathway_forte.constants)

G

GENESET_COLUMN_NAMES (in module pathway_forte.constants)

M

make_classifier_results_directory() (in module pathway_forte.constants) make_gsea_export_directories() (in module pathway_forte.constants) make_ssgsea_export_directories() (in module pathway_forte.constants)

mappings (in module pathway_forte) MSIG_GSEA (in module pathway_forte.constants) MSIG_SSGSEA (in module pathway_forte.constants) multiclass (in module pathway_forte.prediction)

P

pathway_forte (module) pathway_forte-fcs-gsea command line option -d, --data <data> -p, --permutations <permutations> pathway_forte-fcs-gsea-msig command line option -d, --data <data> pathway_forte-fcs-ssgsea command line option -d, --data <data> pathway_forte-ora-hypergeometric command line option --no-threshold -d, --genesets <genesets> -o, --output <output> -s, --fold-changes <fold_changes> pathway_forte-prediction-binary command line option --inner-cv <inner_cv> --outer-cv <outer_cv> --turn-off-warnings -d, --data <data> -i, --max_iterations <max_iterations> pathway_forte-prediction-subtype command line option --chain-pca --explained-variance <explained_variance> --inner-cv <inner_cv> --outer-cv <outer_cv> --turn-off-warnings -d, --ssgsea <ssgsea> -s, --subtypes <subtypes>

pathway_forte-prediction-survival command line option --inner-cv <inner_cv> --outer-cv <outer_cv> --turn-off-warnings -d, --data <data> pathway_forte-prediction-test-stability-prediction command line option --inner-cv <inner_cv> --outer-cv <outer_cv> --turn-off-warnings -i, --max_iterations <max_iterations> -p, --phenotypes-path <phenotypes_path> -s, --ssgsea-scores-path <ssgsea_scores_path> pathway_forte.constants (module) pathway_forte.pipeline (module)

S

survival (in module pathway_forte.prediction)

U

utils (in module pathway_forte.prediction), [1]