Index A | B | C | D | E | F | G | I | J | K | M | N | P | R | S | T | U A agg_jaccard() (in module kstar.helpers) align_sites() (kstar.mapping.ExperimentMapper method) assess_work_dir() (kstar.prune.Pruner method) averageUniqueSubstrates_KSTAR() (in module kstar.analysis.coverage) B build_multiple_compendia_networks() (kstar.prune.Pruner method) build_multiple_networks() (kstar.prune.Pruner method) build_pruned_network() (kstar.prune.Pruner method) C calculate_compendia_sizes() (kstar.prune.Pruner method) calculate_jaccard_by_binary() (in module kstar.helpers) calculate_jaccard_by_sets() (in module kstar.helpers) calculate_kinase_activities() (kstar.calculate.KinaseActivity method) check_configuration() (in module kstar.config) check_data_columns() (kstar.calculate.KinaseActivity method) checkParameters() (kstar.prune.Pruner method) clean_work_dir() (kstar.prune.Pruner method) cluster() (kstar.plot.DotPlot method) compendia_pruned_network() (kstar.prune.Pruner method) context() (kstar.plot.DotPlot method) convert_acc_to_uniprot() (in module kstar.helpers) create_binary_evidence() (kstar.calculate.KinaseActivity method) create_dotplot() (kstar.plot.KSTAR_PDF method) D DotPlot (class in kstar.plot) dotplot() (kstar.plot.DotPlot method) dotplot_page() (kstar.plot.KSTAR_PDF method) drop_kinases() (kstar.plot.DotPlot method) drop_kinases_with_no_significance() (kstar.plot.DotPlot method) E enrichment_analysis() (in module kstar.calculate) evidence_count() (kstar.plot.DotPlot method) evidence_count_plot() (kstar.plot.KSTAR_PDF method) evidence_overlap_plot() (kstar.plot.KSTAR_PDF method) evidence_page() (kstar.plot.KSTAR_PDF method) experimentCoverage() (in module kstar.analysis.coverage) ExperimentMapper (class in kstar.mapping) F find_available_networks() (in module kstar.config) footer() (kstar.plot.KSTAR_PDF method) from_kstar() (in module kstar.calculate) from_kstar_nextflow() (in module kstar.calculate) G generate() (kstar.plot.KSTAR_PDF method) get_allowable_threshold() (kstar.calculate.KinaseActivity method) get_experiment() (kstar.mapping.ExperimentMapper method) get_logger() (in module kstar.helpers) get_number_missed_peptides() (kstar.mapping.ExperimentMapper method) get_number_missed_sites() (kstar.mapping.ExperimentMapper method) get_param_dict() (kstar.calculate.KinaseActivity method) get_random_activities() (kstar.calculate.KinaseActivity method) get_reason_for_unmapped() (kstar.mapping.ExperimentMapper method) get_run_information_content() (kstar.calculate.KinaseActivity method) get_sequence() (kstar.mapping.ExperimentMapper method) getMaximumKinaseSize() (kstar.prune.Pruner method) getRecommendedKinaseSize() (kstar.prune.Pruner method) getStudyBiasDistribution_InExperiment() (in module kstar.analysis.coverage) getStudyBiasDistribution_InPhosphoproteome() (in module kstar.analysis.coverage) getStudyBiasDistribution_InSample() (in module kstar.analysis.coverage) getSubstrateInfluence() (in module kstar.analysis.interactions) getSubstrateInfluence_inExperiment() (in module kstar.analysis.interactions) I install_network_files() (in module kstar.config) J jaci_matrix_between_samples() (in module kstar.helpers) K kinase_mutual_information() (in module kstar.analysis.kinase_MI) KinaseActivity (class in kstar.calculate) kstar module kstar.analysis.coverage module kstar.analysis.interactions module kstar.analysis.kinase_MI module kstar.calculate module, [1] kstar.config module kstar.dataset_processing.accessions module kstar.dataset_processing.peptides module kstar.helpers module kstar.prune module KSTAR_PDF (class in kstar.plot) M make_complete_dotplot() (kstar.plot.DotPlot method) make_dotplot() (kstar.calculate.KinaseActivity method) make_summary_pdf() (kstar.calculate.KinaseActivity method) Mann_Whitney_analysis() (in module kstar.calculate) module kstar kstar.analysis.coverage kstar.analysis.interactions kstar.analysis.kinase_MI kstar.calculate, [1] kstar.config kstar.dataset_processing.accessions kstar.dataset_processing.peptides kstar.helpers kstar.prune N numUniqueSubstrates() (in module kstar.analysis.coverage) P parse_network_information() (in module kstar.helpers) plot_kinase_heatmap() (in module kstar.analysis.kinase_MI) pregenerate_random_activities() (kstar.prune.Pruner method) process_fasta_file() (in module kstar.helpers) Pruner (class in kstar.prune) R randomized_analysis() (in module kstar.calculate) recommend_threshold() (kstar.calculate.KinaseActivity method) report_info() (kstar.prune.Pruner method) report_warning() (kstar.prune.Pruner method) run() (kstar.prune.Pruner method) run_kstar_analysis() (in module kstar.calculate) run_pruning() (in module kstar.prune) S sampleCoverage() (in module kstar.analysis.coverage) save_experiment() (kstar.mapping.ExperimentMapper method) save_kstar() (in module kstar.calculate) save_networks() (kstar.prune.Pruner method) save_run_information() (kstar.prune.Pruner method) set_colors() (kstar.plot.DotPlot method) set_data_columns() (kstar.calculate.KinaseActivity method) (kstar.mapping.ExperimentMapper method) string_to_boolean() (in module kstar.helpers) summary_page() (kstar.plot.KSTAR_PDF method) T table() (kstar.plot.KSTAR_PDF method) test_threshold() (kstar.calculate.KinaseActivity method) test_threshold_range() (kstar.calculate.KinaseActivity method) top_kinases_table() (kstar.plot.KSTAR_PDF method) U update_configuration() (in module kstar.config) update_network_directory() (in module kstar.config)