Index

A

add_features() (ms2rescore.feature_generators.basic.BasicFeatureGenerator method) (ms2rescore.feature_generators.deeplc.DeepLCFeatureGenerator method) (ms2rescore.feature_generators.ionmob.IonMobFeatureGenerator method) (ms2rescore.feature_generators.maxquant.MaxQuantFeatureGenerator method) (ms2rescore.feature_generators.ms2pip.MS2PIPFeatureGenerator method)

add_peptide_confidence() (in module ms2rescore.rescoring_engines.mokapot) add_psm_confidence() (in module ms2rescore.rescoring_engines.mokapot) allowed_modifications (ms2rescore.feature_generators.ionmob.IonMobFeatureGenerator property)

B

BasicFeatureGenerator (class in ms2rescore.feature_generators.basic)

C

calculate_ccs_shift() (ms2rescore.feature_generators.ionmob.IonMobFeatureGenerator method)

calculate_feature_qvalues() (in module ms2rescore.report.charts) convert_psm_list() (in module ms2rescore.rescoring_engines.mokapot)

D

DeepLCFeatureGenerator (class in ms2rescore.feature_generators.deeplc)

F

fdr_plot() (in module ms2rescore.report.charts) fdr_plot_comparison() (in module ms2rescore.report.charts) feature_ecdf_auc_bar() (in module ms2rescore.report.charts) feature_names (ms2rescore.feature_generators.basic.BasicFeatureGenerator attribute) (ms2rescore.feature_generators.deeplc.DeepLCFeatureGenerator attribute) (ms2rescore.feature_generators.maxquant.MaxQuantFeatureGenerator attribute) (ms2rescore.feature_generators.ms2pip.MS2PIPFeatureGenerator attribute)

feature_weights() (in module ms2rescore.report.charts) feature_weights_by_generator() (in module ms2rescore.report.charts) FeatureGeneratorBase (class in ms2rescore.feature_generators.base) FeatureGeneratorException

G

generate_report() (in module ms2rescore.report.generate)

I

identification_overlap() (in module ms2rescore.report.charts)

IonmobException IonMobFeatureGenerator (class in ms2rescore.feature_generators.ionmob)

M

MaxQuantFeatureGenerator (class in ms2rescore.feature_generators.maxquant) MissingMetadataError module ms2rescore ms2rescore.feature_generators ms2rescore.feature_generators.base ms2rescore.feature_generators.basic ms2rescore.feature_generators.deeplc ms2rescore.feature_generators.ionmob ms2rescore.feature_generators.maxquant ms2rescore.feature_generators.ms2pip ms2rescore.report ms2rescore.report.charts ms2rescore.report.generate ms2rescore.rescoring_engines ms2rescore.rescoring_engines.mokapot ms2rescore.rescoring_engines.percolator ms2pip_correlation() (in module ms2rescore.report.charts) MS2PIPFeatureGenerator (class in ms2rescore.feature_generators.ms2pip) ms2rescore module ms2rescore.feature_generators module ms2rescore.feature_generators.base module

ms2rescore.feature_generators.basic module ms2rescore.feature_generators.deeplc module ms2rescore.feature_generators.FEATURE_GENERATORS (in module ms2rescore.feature_generators) ms2rescore.feature_generators.ionmob module ms2rescore.feature_generators.maxquant module ms2rescore.feature_generators.ms2pip module ms2rescore.report module ms2rescore.report.charts module ms2rescore.report.generate module ms2rescore.rescoring_engines module ms2rescore.rescoring_engines.mokapot module ms2rescore.rescoring_engines.percolator module

P

parse_configurations() (in module ms2rescore)

pp_plot() (in module ms2rescore.report.charts)

R

rescore() (in module ms2rescore) (in module ms2rescore.rescoring_engines.mokapot) (in module ms2rescore.rescoring_engines.percolator)

S

save_model_weights() (in module ms2rescore.rescoring_engines.mokapot)

score_histogram() (in module ms2rescore.report.charts) score_scatter_plot() (in module ms2rescore.report.charts)

T

tokenize_peptidoform() (ms2rescore.feature_generators.ionmob.IonMobFeatureGenerator static method)