ABOUT.md
LICENSE
MANIFEST.in
README.md
setup.py
mantis_ml/__init__.py
mantis_ml/config_class.py
mantis_ml.egg-info/PKG-INFO
mantis_ml.egg-info/SOURCES.txt
mantis_ml.egg-info/dependency_links.txt
mantis_ml.egg-info/entry_points.txt
mantis_ml.egg-info/requires.txt
mantis_ml.egg-info/top_level.txt
mantis_ml/conf/.config
mantis_ml/conf/ALS_config.yaml
mantis_ml/conf/CKD_config.yaml
mantis_ml/conf/Epilepsy_config.yaml
mantis_ml/data/README.md
mantis_ml/data/HPO/ALL_SOURCES_ALL_FREQUENCIES_genes_to_phenotype.txt
mantis_ml/data/HPO/ALL_SOURCES_FREQUENT_FEATURES_genes_to_phenotype.txt
mantis_ml/data/HPO/README.md
mantis_ml/data/HPO/process_human_phenotypes.py
mantis_ml/data/adipose_eqtl/README.md
mantis_ml/data/adipose_eqtl/adipose_eQTL.csv
mantis_ml/data/adipose_eqtl/cis_eqtl_column.txt
mantis_ml/data/adipose_eqtl/gwas_locus_column.txt
mantis_ml/data/adipose_eqtl/mmc3.xlsx
mantis_ml/data/adipose_eqtl/process_adipose_eqtl.py
mantis_ml/data/ckddb/26317775a_Hsapiens_CKD_Kidney.csv
mantis_ml/data/ckddb/26317775b_Hsapiens_CKD_Kidney.csv
mantis_ml/data/ckddb/CKDdb_annotation_features.tsv
mantis_ml/data/ensembl/hgnc_to_ens_gids.txt
mantis_ml/data/ensembl/process_hsa37_gtf.py
mantis_ml/data/essential_genes_for_mouse/README.md
mantis_ml/data/essential_genes_for_mouse/compiled_essential_mouse_features.tsv
mantis_ml/data/essential_genes_for_mouse/essential_mouse_gene_features.tsv
mantis_ml/data/essential_genes_for_mouse/essential_mouse_gene_features.tsv.tmp
mantis_ml/data/essential_genes_for_mouse/journal.pgen.1003484.s022.xls
mantis_ml/data/exSNP/CAD_eQTL_hits.csv
mantis_ml/data/exSNP/HT_eQTL_hits.csv
mantis_ml/data/exSNP/README.md
mantis_ml/data/exSNP/WTCCC_DZ_allc_allp_GSeQTL_0.05cM_list_CAD.txt
mantis_ml/data/exSNP/WTCCC_DZ_allc_allp_GSeQTL_0.05cM_list_HT.txt
mantis_ml/data/exSNP/parse_eqtl_file.py
mantis_ml/data/exac-broadinstitute/README_fordist_cleaned_exac_r03_z_data_pLI_2016_01_13.txt
mantis_ml/data/exac-broadinstitute/all_genes.tmp
mantis_ml/data/exac-broadinstitute/all_genes_exac-broad_feature_table.txt
mantis_ml/data/exac-broadinstitute/all_hgnc_genes.txt
mantis_ml/data/exac-broadinstitute/fordist_cleaned_exac_r03_march16_z_pli_rec_null_data.txt
mantis_ml/data/exac-broadinstitute/cnv/README.md
mantis_ml/data/exac-broadinstitute/cnv/exac-final-cnv.gene.scores071316
mantis_ml/data/exac-broadinstitute/cnv/process_exac_cnv_table.py
mantis_ml/data/genic-intolerance/GenicIntolerance_v3_12Mar16.txt
mantis_ml/data/genic-intolerance/README.md
mantis_ml/data/genic-intolerance/RVIS_Unpublished_ExAC_May2015.txt
mantis_ml/data/genic-intolerance/RVIS_Unpublished_ExACv2_March2017.txt
mantis_ml/data/genic-intolerance/all_genes_LoF_FDR_ExAC.tsv
mantis_ml/data/genic-intolerance/all_genes_RVIS.tsv
mantis_ml/data/genic-intolerance/all_genes_RVIS_ExAC.tsv
mantis_ml/data/genic-intolerance/all_genes_RVIS_MTR_ExACv2.tsv
mantis_ml/data/genic-intolerance/compiled_genic_intolerance_scores.tsv
mantis_ml/data/gnomad/README.md
mantis_ml/data/gnomad/compiled_gnomad_features.tsv
mantis_ml/data/gnomad/constraint.txt
mantis_ml/data/goa/12_12_2018.goa_human.gaf.local_copy.gz
mantis_ml/data/goa/GOA_Kidney_Research_Priority_feature.tsv
mantis_ml/data/goa/all_human_go_ids.txt
mantis_ml/data/goa/full_human_go_terms.txt
mantis_ml/data/goa/update_human_go_annotation.py
mantis_ml/data/gtex/RNASeq/GTEx_Analysis_2016-01-15_v7_RNASeQCv1.1.8_gene_median_tpm.gct
mantis_ml/data/gtex/RNASeq/process_gtex_rnaseq_data.py
mantis_ml/data/gwas_catalog/All_genes_GWAS_features.tsv
mantis_ml/data/gwas_catalog/README.md
mantis_ml/data/gwas_catalog/all_associations_v1.0.2.tsv
mantis_ml/data/gwas_catalog/process_gwas_catalog.py
mantis_ml/data/human_protein_atlas/README.md
mantis_ml/data/human_protein_atlas/collapse_normal_tissue_expression.py
mantis_ml/data/human_protein_atlas/collapse_rna_expression.py
mantis_ml/data/human_protein_atlas/normal_tissue.tsv.gz
mantis_ml/data/human_protein_atlas/rna_tissue.tsv.gz
mantis_ml/data/in_web/README.md
mantis_ml/data/in_web/decouple_info_from_inweb_mitab.py
mantis_ml/data/in_web/experimental_pairwise_interactions.tsv
mantis_ml/data/in_web/inferred_pairwise_interactions.tsv
mantis_ml/data/in_web/inweb_pairwise_gene_interactions.tsv
mantis_ml/data/in_web/process_inweb_data.py
mantis_ml/data/mgi/HMD_HumanPhenotype.rpt
mantis_ml/data/mgi/MGI_LethalityPhenotypes.txt
mantis_ml/data/mgi/VOC_MammalianPhenotype.rpt
mantis_ml/data/mgi/hmd_human_pheno.processed.rpt
mantis_ml/data/mgi/mgi_essential_genes.tsv
mantis_ml/data/mgi/process_mgi_files.py
mantis_ml/data/msigdb/tables_per_gene_set/c5.all.v6.2.symbols.gmt
mantis_ml/data/neph_qtl/README.md
mantis_ml/data/neph_qtl/glom_GeneSummary_FDR_0.01.csv
mantis_ml/data/neph_qtl/glom_feature_table.csv
mantis_ml/data/neph_qtl/tub_GeneSummary_FDR_0.01.csv
mantis_ml/data/neph_qtl/tub_feature_table.csv
mantis_ml/data/omim/AD_genes.txt
mantis_ml/data/omim/AD_only_genes.txt
mantis_ml/data/omim/AR_genes.txt
mantis_ml/data/omim/AR_only_genes.txt
mantis_ml/data/omim/All_genes.txt
mantis_ml/data/omim/README.md
mantis_ml/data/omim/autosomal_dominant_recessive_mim_nums.txt
mantis_ml/data/omim/process_edited_genemap2.py
mantis_ml/data/omim/update_omim_dump.py
mantis_ml/data/platelets_eqtl/README.md
mantis_ml/data/platelets_eqtl/platelets_eQTL.csv
mantis_ml/data/platelets_eqtl/process_platelets_eqtl.py
mantis_ml/data/rvis_plosgen_2013/rvis_dataset_S1.csv
mantis_ml/data/rvis_plosgen_2013/rvis_dataset_S2.csv
mantis_ml/modules/__init__.py
mantis_ml/modules/benchmarking/__init__.py
mantis_ml/modules/benchmarking/assess_iterations_num_on_clf_performance.py
mantis_ml/modules/benchmarking/benchmarking_collapsing_hypergeom_enrichment.py
mantis_ml/modules/benchmarking/compare_random_vs_real_seed_results.py
mantis_ml/modules/benchmarking/estimate_predictive_power_of_GMS_score.py
mantis_ml/modules/benchmarking/get_consensus_novel_predictions.py
mantis_ml/modules/hypergeom_enrichment/__init__.py
mantis_ml/modules/hypergeom_enrichment/__main__.py
mantis_ml/modules/hypergeom_enrichment/consensus_predictions.py
mantis_ml/modules/hypergeom_enrichment/updated_benchmark_module.py
mantis_ml/modules/main/__init__.py
mantis_ml/modules/main/__main__.py
mantis_ml/modules/main/test.py
mantis_ml/modules/main/tt.py
mantis_ml/modules/post_processing/__init__.py
mantis_ml/modules/post_processing/evaluate_classifier_predictions.py
mantis_ml/modules/post_processing/merge_predictions_from_classifiers.py
mantis_ml/modules/post_processing/process_classifier_results.py
mantis_ml/modules/post_processing/pyupset.py
mantis_ml/modules/pre_processing/__init__.py
mantis_ml/modules/pre_processing/eda.py
mantis_ml/modules/pre_processing/eda_wrapper.py
mantis_ml/modules/pre_processing/feature_table_compiler.py
mantis_ml/modules/pre_processing/data_compilation/__init__.py
mantis_ml/modules/pre_processing/data_compilation/process_cardiov_specific_features.py
mantis_ml/modules/pre_processing/data_compilation/process_ckd_specific_features.py
mantis_ml/modules/pre_processing/data_compilation/process_features_filtered_by_disease.py
mantis_ml/modules/pre_processing/data_compilation/process_generic_features.py
mantis_ml/modules/profiler/__init__.py
mantis_ml/modules/profiler/__main__.py
mantis_ml/modules/supervised_learn/__init__.py
mantis_ml/modules/supervised_learn/classifiers/__init__.py
mantis_ml/modules/supervised_learn/classifiers/dnn.py
mantis_ml/modules/supervised_learn/classifiers/ensemble_lib.py
mantis_ml/modules/supervised_learn/classifiers/ensemble_stacking.py
mantis_ml/modules/supervised_learn/classifiers/generic_classifier.py
mantis_ml/modules/supervised_learn/classifiers/sklearn_extended_classifier.py
mantis_ml/modules/supervised_learn/core/__init__.py
mantis_ml/modules/supervised_learn/core/balanced_datasets_random_generator.py
mantis_ml/modules/supervised_learn/core/map_hgnc_to_ensembl_ids.py
mantis_ml/modules/supervised_learn/core/ml_plot_functions.py
mantis_ml/modules/supervised_learn/core/prepare_train_test_sets.py
mantis_ml/modules/supervised_learn/feature_selection/__init__.py
mantis_ml/modules/supervised_learn/feature_selection/boruta_feature_selection.R
mantis_ml/modules/supervised_learn/feature_selection/boruta_score_aggregator.py
mantis_ml/modules/supervised_learn/feature_selection/run_boruta.py
mantis_ml/modules/supervised_learn/model_selection/__init__.py
mantis_ml/modules/supervised_learn/model_selection/benchmark_all_classifiers.py
mantis_ml/modules/supervised_learn/model_selection/dnn_grid_search_cv.py
mantis_ml/modules/supervised_learn/model_selection/sklearn_grid_search_cv.py
mantis_ml/modules/supervised_learn/pu_learn/__init__.py
mantis_ml/modules/supervised_learn/pu_learn/pu_learning.py
mantis_ml/modules/unsupervised_learn/__init__.py
mantis_ml/modules/unsupervised_learn/dimens_reduction.py
mantis_ml/modules/unsupervised_learn/dimens_reduction_wrapper.py