Index

B

BestPeptideScorer (class in protein_inference.inference.scorers)

BestTwoPeptideScorer (class in protein_inference.inference.scorers)

C

colour_by_group() (protein_inference.network_grapher.NetworkGrapher method)

colour_by_score() (protein_inference.network_grapher.NetworkGrapher method) colour_by_status() (protein_inference.network_grapher.NetworkGrapher method)

D

draw() (protein_inference.network_grapher.NetworkGrapher method)

F

FalseDiscoveryRateCalculator (class in protein_inference.inference.false_discovery_rate_calculator)

FDR() (protein_inference.inference.false_discovery_rate_calculator.FalseDiscoveryRateCalculator method)

G

get_edge_attribute_dict() (protein_inference.problem_network.ProblemNetwork method) get_node_attribute_dict() (protein_inference.problem_network.ProblemNetwork method)

get_output() (protein_inference.protein_inference_runner.ProteinInferenceRunner method) get_peptides() (protein_inference.problem_network.ProblemNetwork method) get_proteins() (protein_inference.problem_network.ProblemNetwork method)

M

module protein_inference.inference.false_discovery_rate_calculator protein_inference.inference.protein_merger protein_inference.inference.scorers protein_inference.network_grapher protein_inference.problem_network protein_inference.processing.processed_psms protein_inference.processing.psms_network_generator protein_inference.processing.psms_network_splitter protein_inference.processing.psms_preprocessor protein_inference.protein_inference_runner protein_inference.table_maker

N

network (protein_inference.problem_network.ProblemNetwork attribute)

NetworkGrapher (class in protein_inference.network_grapher)

P

parallel_apply() (protein_inference.protein_inference_runner.ProteinInferenceRunner method) PEPProductScorer (class in protein_inference.inference.scorers) pick_nodes() (protein_inference.problem_network.ProblemNetwork method) print_edges() (protein_inference.problem_network.ProblemNetwork method) print_nodes() (protein_inference.problem_network.ProblemNetwork method) ProblemNetwork (class in protein_inference.problem_network) ProcessedPSMs (class in protein_inference.processing.processed_psms) protein_inference.inference.false_discovery_rate_calculator module protein_inference.inference.protein_merger module protein_inference.inference.scorers module protein_inference.network_grapher module protein_inference.problem_network module

protein_inference.processing.processed_psms module protein_inference.processing.psms_network_generator module protein_inference.processing.psms_network_splitter module protein_inference.processing.psms_preprocessor module protein_inference.protein_inference_runner module protein_inference.table_maker module ProteinInferenceRunner (class in protein_inference.protein_inference_runner) ProteinMerger (class in protein_inference.inference.protein_merger) PSMsNetworkGenerator (class in protein_inference.processing.psms_network_generator) PSMsNetworkSplitter (class in protein_inference.processing.psms_network_splitter) PSMsPreprocessor (class in protein_inference.processing.psms_preprocessor)

R

run() (protein_inference.inference.scorers.BestPeptideScorer method) (protein_inference.inference.scorers.BestTwoPeptideScorer method) (protein_inference.inference.scorers.PEPProductScorer method) (protein_inference.protein_inference_runner.ProteinInferenceRunner method)

T

TableMaker (class in protein_inference.table_maker)

tag_FDR() (protein_inference.inference.false_discovery_rate_calculator.FalseDiscoveryRateCalculator method) tag_q_value() (protein_inference.inference.false_discovery_rate_calculator.FalseDiscoveryRateCalculator method)

U

update_nodes() (protein_inference.problem_network.ProblemNetwork method)

W

write_tables() (protein_inference.protein_inference_runner.ProteinInferenceRunner method)