PathwayForte
latest
Command Line Interface :
Command Line Interface
Pipeline
Constants
Statistical Enrichment
Over Representation Methods
Functional Class Scoring
Pathway Topology Methods
Predictive Modeling
Binary Prediction
Multi-Class Prediction
Survival Prediction
Utils
Mappings
Mappings Methods
PathwayForte
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Index
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Index
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Symbols
--chain-pca
pathway_forte-prediction-subtype command line option
--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
--explained-variance <explained_variance>
pathway_forte-prediction-subtype command line option
--fold-changes <fold_changes>
pathway_forte-ora-hypergeometric command line option
--genesets <genesets>
pathway_forte-ora-hypergeometric 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
--max_iterations <max_iterations>
pathway_forte-prediction-binary 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
--output <output>
pathway_forte-ora-hypergeometric command line option
--permutations <permutations>
pathway_forte-fcs-gsea command line option
--phenotypes-path <phenotypes_path>
pathway_forte-prediction-test-stability-prediction command line option
--ssgsea <ssgsea>
pathway_forte-prediction-subtype command line option
--ssgsea-scores-path <ssgsea_scores_path>
pathway_forte-prediction-test-stability-prediction command line option
--subtypes <subtypes>
pathway_forte-prediction-subtype 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
pathway_forte-fcs-gsea command line option
pathway_forte-fcs-gsea-msig command line option
pathway_forte-fcs-ssgsea command line option
pathway_forte-ora-hypergeometric command line option
pathway_forte-prediction-binary command line option
pathway_forte-prediction-subtype command line option
pathway_forte-prediction-survival command line option
-i
pathway_forte-prediction-binary command line option
pathway_forte-prediction-test-stability-prediction command line option
-o
pathway_forte-ora-hypergeometric command line option
-p
pathway_forte-fcs-gsea command line option
pathway_forte-prediction-test-stability-prediction command line option
-s
pathway_forte-ora-hypergeometric command line option
pathway_forte-prediction-subtype command line option
pathway_forte-prediction-test-stability-prediction command line option
B
BIO2BEL_DATA_DIR (in module pathway_forte.constants)
C
check_gmt_files() (in module pathway_forte.constants)
compare_database_results() (in module pathway_forte.pathway_enrichment.functional_class)
create_cls_file() (in module pathway_forte.pathway_enrichment.functional_class)
F
filter_gene_exp_data() (in module pathway_forte.pathway_enrichment.functional_class)
filter_gsea_results() (in module pathway_forte.pathway_enrichment.functional_class)
filter_p_value() (in module pathway_forte.pathway_enrichment.over_representation)
G
GENESET_COLUMN_NAMES (in module pathway_forte.constants)
get_analogs_comparison_numbers() (in module pathway_forte.pathway_enrichment.functional_class)
get_equivalent_mappings_dict() (in module pathway_forte.mappings)
get_equivalent_pairs() (in module pathway_forte.mappings)
get_l1_ratios() (in module pathway_forte.prediction.binary)
get_mapping_dict() (in module pathway_forte.mappings)
get_matching_pairs() (in module pathway_forte.pathway_enrichment.functional_class)
get_pairwise_mapping_numbers() (in module pathway_forte.pathway_enrichment.functional_class)
get_pairwise_mappings() (in module pathway_forte.pathway_enrichment.functional_class)
get_pathway_names() (in module pathway_forte.pathway_enrichment.functional_class)
get_pathways_by_resource() (in module pathway_forte.pathway_enrichment.functional_class)
gsea_results_to_filtered_df() (in module pathway_forte.pathway_enrichment.functional_class)
L
load_compath_mapping_dfs() (in module pathway_forte.mappings)
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)
merge_statistics() (in module pathway_forte.pathway_enrichment.functional_class)
module
pathway_forte
pathway_forte.constants
pathway_forte.mappings
pathway_forte.pathway_enrichment.functional_class
pathway_forte.pathway_enrichment.over_representation
pathway_forte.pipeline
pathway_forte.prediction.binary
pathway_forte.prediction.utils
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
--data <data>
--permutations <permutations>
-d
-p
pathway_forte-fcs-gsea-msig command line option
--data <data>
-d
pathway_forte-fcs-ssgsea command line option
--data <data>
-d
pathway_forte-ora-hypergeometric command line option
--fold-changes <fold_changes>
--genesets <genesets>
--no-threshold
--output <output>
-d
-o
-s
pathway_forte-prediction-binary command line option
--data <data>
--inner-cv <inner_cv>
--max_iterations <max_iterations>
--outer-cv <outer_cv>
--turn-off-warnings
-d
-i
pathway_forte-prediction-subtype command line option
--chain-pca
--explained-variance <explained_variance>
--inner-cv <inner_cv>
--outer-cv <outer_cv>
--ssgsea <ssgsea>
--subtypes <subtypes>
--turn-off-warnings
-d
-s
pathway_forte-prediction-survival command line option
--data <data>
--inner-cv <inner_cv>
--outer-cv <outer_cv>
--turn-off-warnings
-d
pathway_forte-prediction-test-stability-prediction command line option
--inner-cv <inner_cv>
--max_iterations <max_iterations>
--outer-cv <outer_cv>
--phenotypes-path <phenotypes_path>
--ssgsea-scores-path <ssgsea_scores_path>
--turn-off-warnings
-i
-p
-s
pathway_forte.constants
module
pathway_forte.mappings
module
pathway_forte.pathway_enrichment.functional_class
module
pathway_forte.pathway_enrichment.over_representation
module
pathway_forte.pipeline
module
pathway_forte.prediction.binary
module
pathway_forte.prediction.utils
module
pathway_names_to_df() (in module pathway_forte.pathway_enrichment.functional_class)
pca_chaining() (in module pathway_forte.prediction.utils)
perform_hypergeometric_test() (in module pathway_forte.pathway_enrichment.over_representation)
R
read_fold_change_df() (in module pathway_forte.pathway_enrichment.over_representation)
rearrange_df_columns() (in module pathway_forte.pathway_enrichment.functional_class)
run_gsea() (in module pathway_forte.pathway_enrichment.functional_class)
run_ssgsea() (in module pathway_forte.pathway_enrichment.functional_class)
S
ssgsea_nes_to_df() (in module pathway_forte.prediction.binary)
survival (in module pathway_forte.prediction)
T
train_elastic_net_model() (in module pathway_forte.prediction.binary)
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