Index

B

B (LinRidgeRegSVD attribute)

C

C (LinRidgeRegSVD attribute) calculate() (in module geno4sd.utils.log_odds) calculate_patient_delta() (in module geno4sd.evolution.Delta.delta) calculate_patient_delta_predefined() (in module geno4sd.evolution.Delta.delta) calculate_patient_delta_sliding_window() (in module geno4sd.evolution.Delta.delta) calculate_patient_delta_sliding_window_driver() (in module geno4sd.evolution.Delta.delta) cancer_analysis() (in module geno4sd.utils.snpeff_tools) cluster_delta (class in geno4sd.evolution.Delta.delta) cluster_patient_delta() (in module geno4sd.evolution.Delta.delta)

coef_ (LinRidgeRegSVD attribute) compute() (in module geno4sd.ml_tools.ReVeaL) (in module geno4sd.ml_tools.rubricoe.rubricoe) compute_curves() (in module geno4sd.ml_tools.rubricoe.rubricoe) compute_feature_counts() (in module geno4sd.ml_tools.rubricoe.rubricoe) compute_mutational_load() (in module geno4sd.ml_tools.ReVeaL) compute_shedding() (in module geno4sd.liquid_biopsy.LSM.LSM) compute_shingle() (in module geno4sd.ml_tools.ReVeaL) compute_top_features() (in module geno4sd.ml_tools.rubricoe.rubricoe)

D

DB (LinRidgeRegSVD attribute)

download_genome() (in module geno4sd.utils.snpeff_tools)

E

eigenDecomposition() (in module geno4sd.utils.clustering_tools)

F

fit() (LinRidgeRegSVD method)

G

geno4sd module geno4sd.evolution module geno4sd.evolution.Delta module geno4sd.evolution.Delta.delta module geno4sd.liquid_biopsy module geno4sd.liquid_biopsy.LSM module geno4sd.liquid_biopsy.LSM.LSM module geno4sd.ml_tools module geno4sd.ml_tools.ReVeaL module geno4sd.ml_tools.rubricoe module geno4sd.ml_tools.rubricoe.feature_ranking module geno4sd.ml_tools.rubricoe.helper_funcs module geno4sd.ml_tools.rubricoe.lreb module

geno4sd.ml_tools.rubricoe.rubricoe module geno4sd.statgen module geno4sd.topology module geno4sd.utils module geno4sd.utils.clustering_tools module geno4sd.utils.log_odds module geno4sd.utils.read_genesets module geno4sd.utils.read_plink module geno4sd.utils.scRNA module geno4sd.utils.snpEff module geno4sd.utils.snpeff_tools module geno4sd.version module getAffinityMatrix() (in module geno4sd.utils.clustering_tools)

L

LinRidgeRegSVD (class in geno4sd.ml_tools.rubricoe.lreb)

M

module geno4sd geno4sd.evolution geno4sd.evolution.Delta geno4sd.evolution.Delta.delta geno4sd.liquid_biopsy geno4sd.liquid_biopsy.LSM geno4sd.liquid_biopsy.LSM.LSM geno4sd.ml_tools geno4sd.ml_tools.ReVeaL geno4sd.ml_tools.rubricoe geno4sd.ml_tools.rubricoe.feature_ranking geno4sd.ml_tools.rubricoe.helper_funcs geno4sd.ml_tools.rubricoe.lreb geno4sd.ml_tools.rubricoe.rubricoe geno4sd.statgen geno4sd.topology geno4sd.utils geno4sd.utils.clustering_tools geno4sd.utils.log_odds geno4sd.utils.read_genesets geno4sd.utils.read_plink geno4sd.utils.scRNA geno4sd.utils.snpEff geno4sd.utils.snpeff_tools geno4sd.version

P

parse_binary_plink() (in module geno4sd.utils.read_plink) parse_vcf() (in module geno4sd.utils.snpeff_tools) permute_labels() (in module geno4sd.ml_tools.ReVeaL) plot_cluster_patient_delta() (in module geno4sd.evolution.Delta.delta)

plot_scores() (in module geno4sd.ml_tools.rubricoe.rubricoe) Power (LinRidgeRegSVD attribute) preprocess_scRNA() (in module geno4sd.utils.scRNA) PVal (LinRidgeRegSVD attribute)

R

rank_features() (in module geno4sd.ml_tools.rubricoe.feature_ranking)

readGMT() (in module geno4sd.utils.read_genesets)

S

save_to_csv() (in module geno4sd.ml_tools.rubricoe.helper_funcs)

save_to_pickle() (in module geno4sd.ml_tools.rubricoe.helper_funcs) score_curve() (in module geno4sd.ml_tools.rubricoe.feature_ranking)

T

train_test_split() (in module geno4sd.ml_tools.ReVeaL)

Y

youden_index() (in module geno4sd.ml_tools.rubricoe.feature_ranking)