Index

A

abs() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) ACleavageFragmentPrediction (class in Fred2.Core.Base) ACleavageSitePrediction (class in Fred2.Core.Base) activate_allele_coverage_const() (Fred2.EpitopeSelection.OptiTope.OptiTope method) activate_antigen_coverage_const() (Fred2.EpitopeSelection.OptiTope.OptiTope method) activate_epitope_conservation_const() (Fred2.EpitopeSelection.OptiTope.OptiTope method) add() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) (Fred2.EpitopeAssembly.MosaicVaccine.TabuList method) add_prefix() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) add_suffix() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) AEpitopePrediction (class in Fred2.Core.Base) AExternal (class in Fred2.Core.Base) AExternalCleavageSitePrediction (class in Fred2.CleavagePrediction.External) AExternalEpitopePrediction (class in Fred2.EpitopePrediction.External) AExternalHLATyping (class in Fred2.HLAtyping.External) AHLATyping (class in Fred2.Core.Base) align() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) all() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) Allele (class in Fred2.Core.Allele) any() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) APluginRegister (class in Fred2.Core.Base) append() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) apply() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method)

applymap() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) approximate() (Fred2.EpitopeAssembly.EpitopeAssembly.EpitopeAssembly method) (Fred2.EpitopeAssembly.EpitopeAssembly.EpitopeAssemblyWithSpacer method) (Fred2.EpitopeAssembly.MosaicVaccine.MosaicVaccineTS method) APSSMCleavageFragmentPredictor (class in Fred2.CleavagePrediction.PSSM) APSSMCleavageSitePredictor (class in Fred2.CleavagePrediction.PSSM) APSSMEpitopePrediction (class in Fred2.EpitopePrediction.PSSM) APSSMTAPPrediction (class in Fred2.TAPPrediction.PSSM) ARB (class in Fred2.EpitopePrediction.PSSM) AResult (class in Fred2.Core.Result) as_blocks() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) as_matrix() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) asfreq() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) astype() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) ASVM (class in Fred2.Core.Base) ASVMEpitopePrediction (class in Fred2.EpitopePrediction.SVM) ASVMTAPPrediction (class in Fred2.TAPPrediction.SVM) at (Fred2.Core.Result.AResult attribute) (Fred2.Core.Result.CleavageFragmentPredictionResult attribute) (Fred2.Core.Result.CleavageSitePredictionResult attribute) (Fred2.Core.Result.Distance2SelfResult attribute) (Fred2.Core.Result.EpitopePredictionResult attribute) (Fred2.Core.Result.TAPPredictionResult attribute) at_time() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) ATAPPrediction (class in Fred2.Core.Base) ATHLATES_1_0 (class in Fred2.HLAtyping.External) available_methods() (Fred2.CleavagePrediction.CleavageFragmentPredictorFactory static method) (Fred2.CleavagePrediction.CleavageSitePredictorFactory static method) (Fred2.TAPPrediction.TAPPredictorFactory static method) axes (Fred2.Core.Result.AResult attribute) (Fred2.Core.Result.CleavageFragmentPredictionResult attribute) (Fred2.Core.Result.CleavageSitePredictionResult attribute) (Fred2.Core.Result.Distance2SelfResult attribute) (Fred2.Core.Result.EpitopePredictionResult attribute) (Fred2.Core.Result.TAPPredictionResult attribute)

B

back_transcribe() (Fred2.Core.Peptide.Peptide method) (Fred2.Core.Protein.Protein method) (Fred2.Core.Transcript.Transcript method) between_time() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) bfill() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) BIMAS (class in Fred2.EpitopePrediction.PSSM)

blocks (Fred2.Core.Result.AResult attribute) (Fred2.Core.Result.CleavageFragmentPredictionResult attribute) (Fred2.Core.Result.CleavageSitePredictionResult attribute) (Fred2.Core.Result.Distance2SelfResult attribute) (Fred2.Core.Result.EpitopePredictionResult attribute) (Fred2.Core.Result.TAPPredictionResult attribute) bool() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) boxplot() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method)

C

clean_up() (Fred2.HLAtyping.External.AExternalHLATyping method) (Fred2.HLAtyping.External.ATHLATES_1_0 method) (Fred2.HLAtyping.External.OptiType_1_0 method) (Fred2.HLAtyping.External.Polysolver method) (Fred2.HLAtyping.External.Seq2HLA_2_2 method) clear() (Fred2.EpitopeAssembly.MosaicVaccine.TabuList method) CleavageFragmentPredictionResult (class in Fred2.Core.Result) CleavageFragmentPredictorFactory (class in Fred2.CleavagePrediction) cleavagePos (Fred2.CleavagePrediction.External.AExternalCleavageSitePrediction attribute) (Fred2.CleavagePrediction.External.NetChop_3_1 attribute) (Fred2.CleavagePrediction.PSSM.APSSMCleavageFragmentPredictor attribute) (Fred2.CleavagePrediction.PSSM.APSSMCleavageSitePredictor attribute) (Fred2.CleavagePrediction.PSSM.PCM attribute) (Fred2.CleavagePrediction.PSSM.PSSMGinodi attribute) (Fred2.CleavagePrediction.PSSM.ProteaSMMConsecutive attribute) (Fred2.CleavagePrediction.PSSM.ProteaSMMImmuno attribute) (Fred2.Core.Base.ACleavageFragmentPrediction attribute) (Fred2.Core.Base.ACleavageSitePrediction attribute) CleavagePrediction (module) CleavagePrediction.ANN (module) CleavagePrediction.PSSM (module) CleavageSitePredictionResult (class in Fred2.Core.Result) CleavageSitePredictorFactory (class in Fred2.CleavagePrediction) clip() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) clip_lower() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) clip_upper() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) combine() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) combine_first() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) combineAdd() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) combineMult() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) ComblibSidney2008 (class in Fred2.EpitopePrediction.PSSM) command (Fred2.CleavagePrediction.External.AExternalCleavageSitePrediction attribute) (Fred2.CleavagePrediction.External.NetChop_3_1 attribute) (Fred2.Core.Base.AExternal attribute) (Fred2.EpitopePrediction.External.AExternalEpitopePrediction attribute) (Fred2.EpitopePrediction.External.NetCTLpan_1_1 attribute) (Fred2.EpitopePrediction.External.NetMHCII_2_2 attribute) (Fred2.EpitopePrediction.External.NetMHCIIpan_3_0 attribute) (Fred2.EpitopePrediction.External.NetMHCIIpan_3_1 attribute) (Fred2.EpitopePrediction.External.NetMHC_3_0 attribute) (Fred2.EpitopePrediction.External.NetMHC_3_4 attribute) (Fred2.EpitopePrediction.External.NetMHCpan_2_4 attribute) (Fred2.EpitopePrediction.External.NetMHCpan_2_8 attribute) (Fred2.EpitopePrediction.External.PickPocket_1_1 attribute) (Fred2.HLAtyping.External.AExternalHLATyping attribute) (Fred2.HLAtyping.External.ATHLATES_1_0 attribute) (Fred2.HLAtyping.External.OptiType_1_0 attribute) (Fred2.HLAtyping.External.Polysolver attribute) (Fred2.HLAtyping.External.Seq2HLA_2_2 attribute)

complement() (Fred2.Core.Peptide.Peptide method) (Fred2.Core.Protein.Protein method) (Fred2.Core.Transcript.Transcript method) compound() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) consolidate() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) convert_alleles() (Fred2.Core.Base.AEpitopePrediction method) (Fred2.EpitopePrediction.External.AExternalEpitopePrediction method) (Fred2.EpitopePrediction.External.NetCTLpan_1_1 method) (Fred2.EpitopePrediction.External.NetMHCII_2_2 method) (Fred2.EpitopePrediction.External.NetMHCIIpan_3_0 method) (Fred2.EpitopePrediction.External.NetMHCIIpan_3_1 method) (Fred2.EpitopePrediction.External.NetMHC_3_0 method) (Fred2.EpitopePrediction.External.NetMHC_3_4 method) (Fred2.EpitopePrediction.External.NetMHCpan_2_4 method) (Fred2.EpitopePrediction.External.NetMHCpan_2_8 method) (Fred2.EpitopePrediction.External.PickPocket_1_1 method) (Fred2.EpitopePrediction.PSSM.APSSMEpitopePrediction method) (Fred2.EpitopePrediction.PSSM.ARB method) (Fred2.EpitopePrediction.PSSM.BIMAS method) (Fred2.EpitopePrediction.PSSM.ComblibSidney2008 method) (Fred2.EpitopePrediction.PSSM.Epidemix method) (Fred2.EpitopePrediction.PSSM.Hammer method) (Fred2.EpitopePrediction.PSSM.SMM method) (Fred2.EpitopePrediction.PSSM.SMMPMBEC method) (Fred2.EpitopePrediction.PSSM.Syfpeithi method) (Fred2.EpitopePrediction.PSSM.TEPITOPEpan method) (Fred2.EpitopePrediction.SVM.ASVMEpitopePrediction method) (Fred2.EpitopePrediction.SVM.SVMHC method) (Fred2.EpitopePrediction.SVM.UniTope method) convert_objects() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) copy() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) Core.Allele (module) Core.AResult (module) Core.Base (module) Core.Transcript (module) corr() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) corrwith() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) count() (Fred2.Core.Peptide.Peptide method) (Fred2.Core.Protein.Protein method) (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) (Fred2.Core.Transcript.Transcript method) cov() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) cummax() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) cummin() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) cumprod() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) cumsum() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method)

D

deactivate_allele_coverage_const() (Fred2.EpitopeSelection.OptiTope.OptiTope method) deactivate_antigen_coverage_const() (Fred2.EpitopeSelection.OptiTope.OptiTope method) deactivate_epitope_conservation_const() (Fred2.EpitopeSelection.OptiTope.OptiTope method) delevel() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) describe() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) diff() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) discard() (Fred2.EpitopeAssembly.MosaicVaccine.TabuList method) Distance2SelfResult (class in Fred2.Core.Result) DistanceMatrix (class in Fred2.Distance2Self.DistanceMatrix)

div() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) divide() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) dot() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) drop() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) drop_duplicates() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) dropna() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) dtypes (Fred2.Core.Result.AResult attribute) (Fred2.Core.Result.CleavageFragmentPredictionResult attribute) (Fred2.Core.Result.CleavageSitePredictionResult attribute) (Fred2.Core.Result.Distance2SelfResult attribute) (Fred2.Core.Result.EpitopePredictionResult attribute) (Fred2.Core.Result.TAPPredictionResult attribute) duplicated() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method)

E

empty (Fred2.Core.Result.AResult attribute) (Fred2.Core.Result.CleavageFragmentPredictionResult attribute) (Fred2.Core.Result.CleavageSitePredictionResult attribute) (Fred2.Core.Result.Distance2SelfResult attribute) (Fred2.Core.Result.EpitopePredictionResult attribute) (Fred2.Core.Result.TAPPredictionResult attribute) encode() (Fred2.Core.Base.ASVM method) (Fred2.EpitopePrediction.SVM.ASVMEpitopePrediction method) (Fred2.EpitopePrediction.SVM.SVMHC method) (Fred2.EpitopePrediction.SVM.UniTope method) (Fred2.TAPPrediction.SVM.ASVMTAPPrediction method) (Fred2.TAPPrediction.SVM.SVMTAP method) endswith() (Fred2.Core.Peptide.Peptide method) (Fred2.Core.Protein.Protein method) (Fred2.Core.Transcript.Transcript method) Epidemix (class in Fred2.EpitopePrediction.PSSM) EpitopeAssembly (class in Fred2.EpitopeAssembly.EpitopeAssembly) EpitopeAssembly.EpitopeAssembly (module) EpitopeAssembly.MosaicVaccine (module) EpitopeAssemblyWithSpacer (class in Fred2.EpitopeAssembly.EpitopeAssembly)

EpitopePrediction.ANN (module) EpitopePrediction.PSSM (module) EpitopePrediction.SVM (module) EpitopePredictionResult (class in Fred2.Core.Result) eq() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) equals() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) eval() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) exists() (Fred2.IO.UniProtAdapter.UniProtDB method)

F

ffill() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) fillna() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) filter() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) filter_result() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) find() (Fred2.Core.Peptide.Peptide method) (Fred2.Core.Protein.Protein method) (Fred2.Core.Transcript.Transcript method) first() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) first_valid_index() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) floordiv() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) Fred2.CleavagePrediction (module) Fred2.CleavagePrediction.External (module) Fred2.CleavagePrediction.PSSM (module) Fred2.Core.Allele (module) Fred2.Core.Base (module) Fred2.Core.Generator (module) Fred2.Core.Peptide (module) Fred2.Core.Protein (module) Fred2.Core.Result (module) Fred2.Core.Transcript (module) Fred2.Core.Variant (module) Fred2.Distance2Self (module)

Fred2.Distance2Self.DistanceMatrix (module) Fred2.EpitopeAssembly.EpitopeAssembly (module) Fred2.EpitopeAssembly.MosaicVaccine (module) Fred2.EpitopePrediction.External (module) Fred2.EpitopePrediction.PSSM (module) Fred2.EpitopePrediction.SVM (module) Fred2.HLAtyping.External (module) Fred2.IO.FileReader (module) Fred2.IO.MartsAdapter (module) Fred2.IO.RefSeqAdapter (module) Fred2.IO.UniProtAdapter (module) Fred2.TAPPrediction (module) Fred2.TAPPrediction.PSSM (module) Fred2.TAPPrediction.SVM (module) from_csv() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) from_dict() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) from_file() (Fred2.Distance2Self.DistanceMatrix.DistanceMatrix method) from_items() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) from_records() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) ftypes (Fred2.Core.Result.AResult attribute) (Fred2.Core.Result.CleavageFragmentPredictionResult attribute) (Fred2.Core.Result.CleavageSitePredictionResult attribute) (Fred2.Core.Result.Distance2SelfResult attribute) (Fred2.Core.Result.EpitopePredictionResult attribute) (Fred2.Core.Result.TAPPredictionResult attribute)

G

ge() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) generate_peptides_from_proteins() (in module Fred2.Core.Generator) generate_peptides_from_variants() (in module Fred2.Core.Generator) generate_proteins_from_transcripts() (in module Fred2.Core.Generator) generate_transcripts_from_tumor_variants() (in module Fred2.Core.Generator) generate_transcripts_from_variants() (in module Fred2.Core.Generator) get() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) get_all_proteins() (Fred2.Core.Peptide.Peptide method) get_all_transcripts() (Fred2.Core.Peptide.Peptide method) get_all_variant_gene() (Fred2.IO.MartsAdapter.MartsAdapter method) get_all_variant_ids() (Fred2.IO.MartsAdapter.MartsAdapter method) get_annotated_protein_pos() (Fred2.Core.Variant.Variant method) get_annotated_transcript_pos() (Fred2.Core.Variant.Variant method) get_dtype_counts() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) get_external_version() (Fred2.CleavagePrediction.External.AExternalCleavageSitePrediction method) (Fred2.CleavagePrediction.External.NetChop_3_1 method) (Fred2.Core.Base.AExternal method) (Fred2.EpitopePrediction.External.AExternalEpitopePrediction method) (Fred2.EpitopePrediction.External.NetCTLpan_1_1 method) (Fred2.EpitopePrediction.External.NetMHCII_2_2 method) (Fred2.EpitopePrediction.External.NetMHCIIpan_3_0 method) (Fred2.EpitopePrediction.External.NetMHCIIpan_3_1 method) (Fred2.EpitopePrediction.External.NetMHC_3_0 method) (Fred2.EpitopePrediction.External.NetMHC_3_4 method) (Fred2.EpitopePrediction.External.NetMHCpan_2_4 method) (Fred2.EpitopePrediction.External.NetMHCpan_2_8 method) (Fred2.EpitopePrediction.External.PickPocket_1_1 method) (Fred2.HLAtyping.External.AExternalHLATyping method) (Fred2.HLAtyping.External.ATHLATES_1_0 method) (Fred2.HLAtyping.External.OptiType_1_0 method) (Fred2.HLAtyping.External.Polysolver method) (Fred2.HLAtyping.External.Seq2HLA_2_2 method) get_ftype_counts() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) get_metadata() (Fred2.Core.Allele.Allele method) (Fred2.Core.Base.MetadataLogger method) (Fred2.Core.Peptide.Peptide method) (Fred2.Core.Protein.Protein method) (Fred2.Core.Transcript.Transcript method) (Fred2.Core.Variant.Variant method) get_product_sequence() (Fred2.IO.MartsAdapter.MartsAdapter method) (Fred2.IO.RefSeqAdapter.RefSeqAdapter method) get_protein() (Fred2.Core.Peptide.Peptide method)

get_protein_positions() (Fred2.Core.Peptide.Peptide method) get_protein_sequence_from_protein_id() (Fred2.IO.MartsAdapter.MartsAdapter method) get_shift() (Fred2.Core.Variant.Variant method) get_transcript() (Fred2.Core.Peptide.Peptide method) get_transcript_information() (Fred2.IO.MartsAdapter.MartsAdapter method) (Fred2.IO.RefSeqAdapter.RefSeqAdapter method) get_transcript_information_from_protein_id() (Fred2.IO.MartsAdapter.MartsAdapter method) get_transcript_offset() (Fred2.Core.Variant.Variant method) get_transcript_position() (Fred2.IO.MartsAdapter.MartsAdapter method) get_transcript_sequence() (Fred2.IO.MartsAdapter.MartsAdapter method) (Fred2.IO.RefSeqAdapter.RefSeqAdapter method) get_value() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) get_values() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) get_variant_gene() (Fred2.IO.MartsAdapter.MartsAdapter method) get_variant_id_from_gene_id() (Fred2.IO.MartsAdapter.MartsAdapter method) get_variant_id_from_protein_id() (Fred2.IO.MartsAdapter.MartsAdapter method) get_variant_ids() (Fred2.IO.MartsAdapter.MartsAdapter method) get_variants_by_protein() (Fred2.Core.Peptide.Peptide method) get_variants_by_protein_position() (Fred2.Core.Peptide.Peptide method) groupby() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) gt() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method)

H

Hammer (class in Fred2.EpitopePrediction.PSSM) head() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method)

hist() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) HLAtyping.External (module)

I

iat (Fred2.Core.Result.AResult attribute) (Fred2.Core.Result.CleavageFragmentPredictionResult attribute) (Fred2.Core.Result.CleavageSitePredictionResult attribute) (Fred2.Core.Result.Distance2SelfResult attribute) (Fred2.Core.Result.EpitopePredictionResult attribute) (Fred2.Core.Result.TAPPredictionResult attribute) icol() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) idxmax() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) idxmin() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) iget_value() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) iloc (Fred2.Core.Result.AResult attribute) (Fred2.Core.Result.CleavageFragmentPredictionResult attribute) (Fred2.Core.Result.CleavageSitePredictionResult attribute) (Fred2.Core.Result.Distance2SelfResult attribute) (Fred2.Core.Result.EpitopePredictionResult attribute) (Fred2.Core.Result.TAPPredictionResult attribute) info() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) insert() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) interpolate() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) IO.MartsAdapter (module) IO.niProtAdapter (module) IO.RefSeqAdapter (module)

irow() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) is_copy (Fred2.Core.Result.AResult attribute) (Fred2.Core.Result.CleavageFragmentPredictionResult attribute) (Fred2.Core.Result.CleavageSitePredictionResult attribute) (Fred2.Core.Result.Distance2SelfResult attribute) (Fred2.Core.Result.EpitopePredictionResult attribute) (Fred2.Core.Result.TAPPredictionResult attribute) is_in_path() (Fred2.CleavagePrediction.External.AExternalCleavageSitePrediction method) (Fred2.CleavagePrediction.External.NetChop_3_1 method) (Fred2.Core.Base.AExternal method) (Fred2.EpitopePrediction.External.AExternalEpitopePrediction method) (Fred2.EpitopePrediction.External.NetCTLpan_1_1 method) (Fred2.EpitopePrediction.External.NetMHCII_2_2 method) (Fred2.EpitopePrediction.External.NetMHCIIpan_3_0 method) (Fred2.EpitopePrediction.External.NetMHCIIpan_3_1 method) (Fred2.EpitopePrediction.External.NetMHC_3_0 method) (Fred2.EpitopePrediction.External.NetMHC_3_4 method) (Fred2.EpitopePrediction.External.NetMHCpan_2_4 method) (Fred2.EpitopePrediction.External.NetMHCpan_2_8 method) (Fred2.EpitopePrediction.External.PickPocket_1_1 method) (Fred2.HLAtyping.External.AExternalHLATyping method) (Fred2.HLAtyping.External.ATHLATES_1_0 method) (Fred2.HLAtyping.External.OptiType_1_0 method) (Fred2.HLAtyping.External.Polysolver method) (Fred2.HLAtyping.External.Seq2HLA_2_2 method) isdisjoint() (Fred2.EpitopeAssembly.MosaicVaccine.TabuList method) isin() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) isnull() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) iteritems() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) iterkv() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) iterrows() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) itertuples() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) ix (Fred2.Core.Result.AResult attribute) (Fred2.Core.Result.CleavageFragmentPredictionResult attribute) (Fred2.Core.Result.CleavageSitePredictionResult attribute) (Fred2.Core.Result.Distance2SelfResult attribute) (Fred2.Core.Result.EpitopePredictionResult attribute) (Fred2.Core.Result.TAPPredictionResult attribute)

J

join() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method)

K

keys() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) kurt() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method)

kurtosis() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method)

L

last() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) last_valid_index() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) le() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) load() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) (Fred2.IO.RefSeqAdapter.RefSeqAdapter method) loc (Fred2.Core.Result.AResult attribute) (Fred2.Core.Result.CleavageFragmentPredictionResult attribute) (Fred2.Core.Result.CleavageSitePredictionResult attribute) (Fred2.Core.Result.Distance2SelfResult attribute) (Fred2.Core.Result.EpitopePredictionResult attribute) (Fred2.Core.Result.TAPPredictionResult attribute)

log_metadata() (Fred2.Core.Allele.Allele method) (Fred2.Core.Base.MetadataLogger method) (Fred2.Core.Peptide.Peptide method) (Fred2.Core.Protein.Protein method) (Fred2.Core.Transcript.Transcript method) (Fred2.Core.Variant.Variant method) lookup() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) lower() (Fred2.Core.Peptide.Peptide method) (Fred2.Core.Protein.Protein method) (Fred2.Core.Transcript.Transcript method) lstrip() (Fred2.Core.Peptide.Peptide method) (Fred2.Core.Protein.Protein method) (Fred2.Core.Transcript.Transcript method) lt() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method)

M

mad() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) MartsAdapter (class in Fred2.IO.MartsAdapter) mask() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) max() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) mean() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) median() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) merge() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) merge_results() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) MetadataLogger (class in Fred2.Core.Base)

min() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) mod() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) mode() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) MosaicVaccineTS (class in Fred2.EpitopeAssembly.MosaicVaccine) mro() (Fred2.Core.Base.APluginRegister method) mul() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) multiply() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) MutationSyntax (class in Fred2.Core.Variant)

N

name (Fred2.CleavagePrediction.External.AExternalCleavageSitePrediction attribute) (Fred2.CleavagePrediction.External.NetChop_3_1 attribute) (Fred2.CleavagePrediction.PSSM.APSSMCleavageFragmentPredictor attribute) (Fred2.CleavagePrediction.PSSM.APSSMCleavageSitePredictor attribute) (Fred2.CleavagePrediction.PSSM.PCM attribute) (Fred2.CleavagePrediction.PSSM.PSSMGinodi attribute) (Fred2.CleavagePrediction.PSSM.ProteaSMMConsecutive attribute) (Fred2.CleavagePrediction.PSSM.ProteaSMMImmuno attribute) (Fred2.Core.Base.ACleavageFragmentPrediction attribute) (Fred2.Core.Base.ACleavageSitePrediction attribute) (Fred2.Core.Base.AEpitopePrediction attribute) (Fred2.Core.Base.AHLATyping attribute) (Fred2.Core.Base.ATAPPrediction attribute) (Fred2.EpitopePrediction.External.AExternalEpitopePrediction attribute) (Fred2.EpitopePrediction.External.NetCTLpan_1_1 attribute) (Fred2.EpitopePrediction.External.NetMHCII_2_2 attribute) (Fred2.EpitopePrediction.External.NetMHCIIpan_3_0 attribute) (Fred2.EpitopePrediction.External.NetMHCIIpan_3_1 attribute) (Fred2.EpitopePrediction.External.NetMHC_3_0 attribute) (Fred2.EpitopePrediction.External.NetMHC_3_4 attribute) (Fred2.EpitopePrediction.External.NetMHCpan_2_4 attribute) (Fred2.EpitopePrediction.External.NetMHCpan_2_8 attribute) (Fred2.EpitopePrediction.External.PickPocket_1_1 attribute) (Fred2.EpitopePrediction.PSSM.APSSMEpitopePrediction attribute) (Fred2.EpitopePrediction.PSSM.ARB attribute) (Fred2.EpitopePrediction.PSSM.BIMAS attribute) (Fred2.EpitopePrediction.PSSM.ComblibSidney2008 attribute) (Fred2.EpitopePrediction.PSSM.Epidemix attribute) (Fred2.EpitopePrediction.PSSM.Hammer attribute) (Fred2.EpitopePrediction.PSSM.SMM attribute) (Fred2.EpitopePrediction.PSSM.SMMPMBEC attribute) (Fred2.EpitopePrediction.PSSM.Syfpeithi attribute) (Fred2.EpitopePrediction.PSSM.TEPITOPEpan attribute) (Fred2.EpitopePrediction.SVM.ASVMEpitopePrediction attribute) (Fred2.EpitopePrediction.SVM.SVMHC attribute) (Fred2.EpitopePrediction.SVM.UniTope attribute) (Fred2.HLAtyping.External.AExternalHLATyping attribute) (Fred2.HLAtyping.External.ATHLATES_1_0 attribute) (Fred2.HLAtyping.External.OptiType_1_0 attribute) (Fred2.HLAtyping.External.Polysolver attribute) (Fred2.HLAtyping.External.Seq2HLA_2_2 attribute) (Fred2.TAPPrediction.PSSM.APSSMTAPPrediction attribute) (Fred2.TAPPrediction.PSSM.SMMTAP attribute) (Fred2.TAPPrediction.PSSM.TAPDoytchinova attribute) (Fred2.TAPPrediction.SVM.ASVMTAPPrediction attribute) (Fred2.TAPPrediction.SVM.SVMTAP attribute) ndim (Fred2.Core.Result.AResult attribute) (Fred2.Core.Result.CleavageFragmentPredictionResult attribute) (Fred2.Core.Result.CleavageSitePredictionResult attribute) (Fred2.Core.Result.Distance2SelfResult attribute) (Fred2.Core.Result.EpitopePredictionResult attribute) (Fred2.Core.Result.TAPPredictionResult attribute) ne() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) NetChop_3_1 (class in Fred2.CleavagePrediction.External) NetCTLpan_1_1 (class in Fred2.EpitopePrediction.External) NetMHC_3_0 (class in Fred2.EpitopePrediction.External) NetMHC_3_4 (class in Fred2.EpitopePrediction.External)

NetMHCII_2_2 (class in Fred2.EpitopePrediction.External) NetMHCIIpan_3_0 (class in Fred2.EpitopePrediction.External) NetMHCIIpan_3_1 (class in Fred2.EpitopePrediction.External) NetMHCpan_2_4 (class in Fred2.EpitopePrediction.External) NetMHCpan_2_8 (class in Fred2.EpitopePrediction.External) newid (Fred2.Core.Protein.Protein attribute) (Fred2.Core.Transcript.Transcript attribute) notnull() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method)

O

OptiTope (class in Fred2.EpitopeSelection.OptiTope)

OptiType_1_0 (class in Fred2.HLAtyping.External)

P

parse_external_result() (Fred2.CleavagePrediction.External.AExternalCleavageSitePrediction method) (Fred2.CleavagePrediction.External.NetChop_3_1 method) (Fred2.Core.Base.AExternal method) (Fred2.EpitopePrediction.External.AExternalEpitopePrediction method) (Fred2.EpitopePrediction.External.NetCTLpan_1_1 method) (Fred2.EpitopePrediction.External.NetMHCII_2_2 method) (Fred2.EpitopePrediction.External.NetMHCIIpan_3_0 method) (Fred2.EpitopePrediction.External.NetMHCIIpan_3_1 method) (Fred2.EpitopePrediction.External.NetMHC_3_0 method) (Fred2.EpitopePrediction.External.NetMHC_3_4 method) (Fred2.EpitopePrediction.External.NetMHCpan_2_4 method) (Fred2.EpitopePrediction.External.NetMHCpan_2_8 method) (Fred2.EpitopePrediction.External.PickPocket_1_1 method) (Fred2.HLAtyping.External.AExternalHLATyping method) (Fred2.HLAtyping.External.ATHLATES_1_0 method) (Fred2.HLAtyping.External.OptiType_1_0 method) (Fred2.HLAtyping.External.Polysolver method) (Fred2.HLAtyping.External.Seq2HLA_2_2 method) PCM (class in Fred2.CleavagePrediction.PSSM) pct_change() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) Peptide (class in Fred2.Core.Peptide) PickPocket_1_1 (class in Fred2.EpitopePrediction.External) pivot() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) pivot_table() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) plot() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) Polysolver (class in Fred2.HLAtyping.External) pop() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) (Fred2.EpitopeAssembly.MosaicVaccine.TabuList method)

pow() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) predict() (Fred2.CleavagePrediction.External.AExternalCleavageSitePrediction method) (Fred2.CleavagePrediction.External.NetChop_3_1 method) (Fred2.CleavagePrediction.PSSM.APSSMCleavageFragmentPredictor method) (Fred2.CleavagePrediction.PSSM.APSSMCleavageSitePredictor method) (Fred2.CleavagePrediction.PSSM.PCM method) (Fred2.CleavagePrediction.PSSM.PSSMGinodi method) (Fred2.CleavagePrediction.PSSM.ProteaSMMConsecutive method) (Fred2.CleavagePrediction.PSSM.ProteaSMMImmuno method) (Fred2.Core.Base.ACleavageFragmentPrediction method) (Fred2.Core.Base.ACleavageSitePrediction method) (Fred2.Core.Base.AEpitopePrediction method) (Fred2.Core.Base.AHLATyping method) (Fred2.Core.Base.ATAPPrediction method) (Fred2.EpitopePrediction.External.AExternalEpitopePrediction method) (Fred2.EpitopePrediction.External.NetCTLpan_1_1 method) (Fred2.EpitopePrediction.External.NetMHCII_2_2 method) (Fred2.EpitopePrediction.External.NetMHCIIpan_3_0 method) (Fred2.EpitopePrediction.External.NetMHCIIpan_3_1 method) (Fred2.EpitopePrediction.External.NetMHC_3_0 method) (Fred2.EpitopePrediction.External.NetMHC_3_4 method) (Fred2.EpitopePrediction.External.NetMHCpan_2_4 method) (Fred2.EpitopePrediction.External.NetMHCpan_2_8 method) (Fred2.EpitopePrediction.External.PickPocket_1_1 method) (Fred2.EpitopePrediction.PSSM.APSSMEpitopePrediction method) (Fred2.EpitopePrediction.PSSM.ARB method) (Fred2.EpitopePrediction.PSSM.BIMAS method) (Fred2.EpitopePrediction.PSSM.ComblibSidney2008 method) (Fred2.EpitopePrediction.PSSM.Epidemix method) (Fred2.EpitopePrediction.PSSM.Hammer method) (Fred2.EpitopePrediction.PSSM.SMM method) (Fred2.EpitopePrediction.PSSM.SMMPMBEC method) (Fred2.EpitopePrediction.PSSM.Syfpeithi method) (Fred2.EpitopePrediction.PSSM.TEPITOPEpan method) (Fred2.EpitopePrediction.SVM.ASVMEpitopePrediction method) (Fred2.EpitopePrediction.SVM.SVMHC method) (Fred2.EpitopePrediction.SVM.UniTope method) (Fred2.HLAtyping.External.AExternalHLATyping method) (Fred2.HLAtyping.External.ATHLATES_1_0 method) (Fred2.HLAtyping.External.OptiType_1_0 method) (Fred2.HLAtyping.External.Polysolver method) (Fred2.HLAtyping.External.Seq2HLA_2_2 method) (Fred2.TAPPrediction.PSSM.APSSMTAPPrediction method) (Fred2.TAPPrediction.PSSM.SMMTAP method) (Fred2.TAPPrediction.PSSM.TAPDoytchinova method) (Fred2.TAPPrediction.SVM.ASVMTAPPrediction method) (Fred2.TAPPrediction.SVM.SVMTAP method) prepare_input() (Fred2.CleavagePrediction.External.AExternalCleavageSitePrediction method) (Fred2.CleavagePrediction.External.NetChop_3_1 method) (Fred2.EpitopePrediction.External.AExternalEpitopePrediction method) (Fred2.EpitopePrediction.External.NetCTLpan_1_1 method) (Fred2.EpitopePrediction.External.NetMHCII_2_2 method) (Fred2.EpitopePrediction.External.NetMHCIIpan_3_0 method) (Fred2.EpitopePrediction.External.NetMHCIIpan_3_1 method) (Fred2.EpitopePrediction.External.NetMHC_3_0 method) (Fred2.EpitopePrediction.External.NetMHC_3_4 method) (Fred2.EpitopePrediction.External.NetMHCpan_2_4 method) (Fred2.EpitopePrediction.External.NetMHCpan_2_8 method) (Fred2.EpitopePrediction.External.PickPocket_1_1 method) prod() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) product() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) ProteaSMMConsecutive (class in Fred2.CleavagePrediction.PSSM) ProteaSMMImmuno (class in Fred2.CleavagePrediction.PSSM) Protein (class in Fred2.Core.Protein) PSSMGinodi (class in Fred2.CleavagePrediction.PSSM)

Q

quantile() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method)

query() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method)

R

radd() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) rank() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) rdiv() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) read_annovar_exonic() (in module Fred2.IO.FileReader) read_fasta() (in module Fred2.IO.FileReader) read_lines() (in module Fred2.IO.FileReader) read_seqs() (Fred2.IO.UniProtAdapter.UniProtDB method) Reader (module) RefSeqAdapter (class in Fred2.IO.RefSeqAdapter) register() (Fred2.Core.Base.APluginRegister method) reindex() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) reindex_axis() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) reindex_like() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) remove() (Fred2.EpitopeAssembly.MosaicVaccine.TabuList method) rename() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method)

rename_axis() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) reorder_levels() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) replace() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) resample() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) reset_index() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) reverse_complement() (Fred2.Core.Peptide.Peptide method) (Fred2.Core.Protein.Protein method) (Fred2.Core.Transcript.Transcript method) rfind() (Fred2.Core.Peptide.Peptide method) (Fred2.Core.Protein.Protein method) (Fred2.Core.Transcript.Transcript method) rfloordiv() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) rmod() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) rmul() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) rpow() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) rsplit() (Fred2.Core.Peptide.Peptide method) (Fred2.Core.Protein.Protein method) (Fred2.Core.Transcript.Transcript method) rstrip() (Fred2.Core.Peptide.Peptide method) (Fred2.Core.Protein.Protein method) (Fred2.Core.Transcript.Transcript method) rsub() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) rtruediv() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method)

S

save() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) search() (Fred2.IO.UniProtAdapter.UniProtDB method) search_all() (Fred2.IO.UniProtAdapter.UniProtDB method) select() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) Seq2HLA_2_2 (class in Fred2.HLAtyping.External) set_index() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) set_k() (Fred2.EpitopeSelection.OptiTope.OptiTope method) set_value() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) shape (Fred2.Core.Result.AResult attribute) (Fred2.Core.Result.CleavageFragmentPredictionResult attribute) (Fred2.Core.Result.CleavageSitePredictionResult attribute) (Fred2.Core.Result.Distance2SelfResult attribute) (Fred2.Core.Result.EpitopePredictionResult attribute) (Fred2.Core.Result.TAPPredictionResult attribute) shift() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) skew() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) SMM (class in Fred2.EpitopePrediction.PSSM) SMMPMBEC (class in Fred2.EpitopePrediction.PSSM) SMMTAP (class in Fred2.TAPPrediction.PSSM) solve() (Fred2.EpitopeAssembly.EpitopeAssembly.EpitopeAssembly method) (Fred2.EpitopeAssembly.EpitopeAssembly.EpitopeAssemblyWithSpacer method) (Fred2.EpitopeAssembly.MosaicVaccine.MosaicVaccineTS method) (Fred2.EpitopeSelection.OptiTope.OptiTope method) sort() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) sort_index() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) sortlevel() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method)

split() (Fred2.Core.Peptide.Peptide method) (Fred2.Core.Protein.Protein method) (Fred2.Core.Transcript.Transcript method) squeeze() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) stack() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) startswith() (Fred2.Core.Peptide.Peptide method) (Fred2.Core.Protein.Protein method) (Fred2.Core.Transcript.Transcript method) std() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) strip() (Fred2.Core.Peptide.Peptide method) (Fred2.Core.Protein.Protein method) (Fred2.Core.Transcript.Transcript method) sub() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) subtract() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) suffixPrefixMatch() (in module Fred2.EpitopeAssembly.MosaicVaccine) sum() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) supportedAlleles (Fred2.Core.Base.AEpitopePrediction attribute) (Fred2.EpitopePrediction.External.AExternalEpitopePrediction attribute) (Fred2.EpitopePrediction.External.NetCTLpan_1_1 attribute) (Fred2.EpitopePrediction.External.NetMHCII_2_2 attribute) (Fred2.EpitopePrediction.External.NetMHCIIpan_3_0 attribute) (Fred2.EpitopePrediction.External.NetMHCIIpan_3_1 attribute) (Fred2.EpitopePrediction.External.NetMHC_3_0 attribute) (Fred2.EpitopePrediction.External.NetMHC_3_4 attribute) (Fred2.EpitopePrediction.External.NetMHCpan_2_4 attribute) (Fred2.EpitopePrediction.External.NetMHCpan_2_8 attribute) (Fred2.EpitopePrediction.External.PickPocket_1_1 attribute) (Fred2.EpitopePrediction.PSSM.APSSMEpitopePrediction attribute) (Fred2.EpitopePrediction.PSSM.ARB attribute) (Fred2.EpitopePrediction.PSSM.BIMAS attribute) (Fred2.EpitopePrediction.PSSM.ComblibSidney2008 attribute) (Fred2.EpitopePrediction.PSSM.Epidemix attribute) (Fred2.EpitopePrediction.PSSM.Hammer attribute) (Fred2.EpitopePrediction.PSSM.SMM attribute) (Fred2.EpitopePrediction.PSSM.SMMPMBEC attribute) (Fred2.EpitopePrediction.PSSM.Syfpeithi attribute) (Fred2.EpitopePrediction.PSSM.TEPITOPEpan attribute) (Fred2.EpitopePrediction.SVM.ASVMEpitopePrediction attribute) (Fred2.EpitopePrediction.SVM.SVMHC attribute) (Fred2.EpitopePrediction.SVM.UniTope attribute) supportedLength (Fred2.CleavagePrediction.External.AExternalCleavageSitePrediction attribute) (Fred2.CleavagePrediction.External.NetChop_3_1 attribute) (Fred2.CleavagePrediction.PSSM.APSSMCleavageFragmentPredictor attribute) (Fred2.CleavagePrediction.PSSM.APSSMCleavageSitePredictor attribute) (Fred2.CleavagePrediction.PSSM.PCM attribute) (Fred2.CleavagePrediction.PSSM.PSSMGinodi attribute) (Fred2.CleavagePrediction.PSSM.ProteaSMMConsecutive attribute) (Fred2.CleavagePrediction.PSSM.ProteaSMMImmuno attribute) (Fred2.Core.Base.ACleavageFragmentPrediction attribute) (Fred2.Core.Base.ACleavageSitePrediction attribute) (Fred2.Core.Base.AEpitopePrediction attribute) (Fred2.Core.Base.ATAPPrediction attribute) (Fred2.EpitopePrediction.External.AExternalEpitopePrediction attribute) (Fred2.EpitopePrediction.External.NetCTLpan_1_1 attribute) (Fred2.EpitopePrediction.External.NetMHCII_2_2 attribute) (Fred2.EpitopePrediction.External.NetMHCIIpan_3_0 attribute) (Fred2.EpitopePrediction.External.NetMHCIIpan_3_1 attribute) (Fred2.EpitopePrediction.External.NetMHC_3_0 attribute) (Fred2.EpitopePrediction.External.NetMHC_3_4 attribute) (Fred2.EpitopePrediction.External.NetMHCpan_2_4 attribute) (Fred2.EpitopePrediction.External.NetMHCpan_2_8 attribute) (Fred2.EpitopePrediction.External.PickPocket_1_1 attribute) (Fred2.EpitopePrediction.PSSM.APSSMEpitopePrediction attribute) (Fred2.EpitopePrediction.PSSM.ARB attribute) (Fred2.EpitopePrediction.PSSM.BIMAS attribute) (Fred2.EpitopePrediction.PSSM.ComblibSidney2008 attribute) (Fred2.EpitopePrediction.PSSM.Epidemix attribute) (Fred2.EpitopePrediction.PSSM.Hammer attribute) (Fred2.EpitopePrediction.PSSM.SMM attribute) (Fred2.EpitopePrediction.PSSM.SMMPMBEC attribute) (Fred2.EpitopePrediction.PSSM.Syfpeithi attribute) (Fred2.EpitopePrediction.PSSM.TEPITOPEpan attribute) (Fred2.EpitopePrediction.SVM.ASVMEpitopePrediction attribute) (Fred2.EpitopePrediction.SVM.SVMHC attribute) (Fred2.EpitopePrediction.SVM.UniTope attribute) (Fred2.TAPPrediction.PSSM.APSSMTAPPrediction attribute) (Fred2.TAPPrediction.PSSM.SMMTAP attribute) (Fred2.TAPPrediction.PSSM.TAPDoytchinova attribute) (Fred2.TAPPrediction.SVM.ASVMTAPPrediction attribute) (Fred2.TAPPrediction.SVM.SVMTAP attribute) SVMHC (class in Fred2.EpitopePrediction.SVM) SVMTAP (class in Fred2.TAPPrediction.SVM) swapaxes() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) swaplevel() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) Syfpeithi (class in Fred2.EpitopePrediction.PSSM)

T

T (Fred2.Core.Result.AResult attribute) (Fred2.Core.Result.CleavageFragmentPredictionResult attribute) (Fred2.Core.Result.CleavageSitePredictionResult attribute) (Fred2.Core.Result.Distance2SelfResult attribute) (Fred2.Core.Result.EpitopePredictionResult attribute) (Fred2.Core.Result.TAPPredictionResult attribute) TabuList (class in Fred2.EpitopeAssembly.MosaicVaccine) tail() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) take() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) TAPDoytchinova (class in Fred2.TAPPrediction.PSSM) TAPPRediction (module) TAPPrediction.PSSM (module) TAPPrediction.SVM (module) TAPPredictionResult (class in Fred2.Core.Result) TAPPredictorFactory (class in Fred2.TAPPrediction) TEPITOPEpan (class in Fred2.EpitopePrediction.PSSM) to_clipboard() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) to_csv() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) to_dense() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) to_dict() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) to_excel() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) to_file() (Fred2.Distance2Self.DistanceMatrix.DistanceMatrix method) to_gbq() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) to_hdf() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) to_html() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) to_json() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) to_latex() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) to_msgpack() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method)

to_panel() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) to_period() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) to_pickle() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) to_records() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) to_sparse() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) to_sql() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) to_stata() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) to_string() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) to_timestamp() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) to_wide() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) tomutable() (Fred2.Core.Peptide.Peptide method) (Fred2.Core.Protein.Protein method) (Fred2.Core.Transcript.Transcript method) tostring() (Fred2.Core.Peptide.Peptide method) (Fred2.Core.Protein.Protein method) (Fred2.Core.Transcript.Transcript method) trailingN (Fred2.CleavagePrediction.PSSM.APSSMCleavageFragmentPredictor attribute) (Fred2.CleavagePrediction.PSSM.PSSMGinodi attribute) tralingC (Fred2.CleavagePrediction.PSSM.APSSMCleavageFragmentPredictor attribute) (Fred2.CleavagePrediction.PSSM.PSSMGinodi attribute) transcribe() (Fred2.Core.Peptide.Peptide method) (Fred2.Core.Protein.Protein method) (Fred2.Core.Transcript.Transcript method) Transcript (class in Fred2.Core.Transcript) translate() (Fred2.Core.Peptide.Peptide method) (Fred2.Core.Protein.Protein method) (Fred2.Core.Transcript.Transcript method) transpose() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) truediv() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) truncate() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) tshift() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) tz_convert() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) tz_localize() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method)

U

ungap() (Fred2.Core.Peptide.Peptide method) (Fred2.Core.Protein.Protein method) (Fred2.Core.Transcript.Transcript method) UniProtDB (class in Fred2.IO.UniProtAdapter) UniTope (class in Fred2.EpitopePrediction.SVM)

unstack() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) update() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) upper() (Fred2.Core.Peptide.Peptide method) (Fred2.Core.Protein.Protein method) (Fred2.Core.Transcript.Transcript method)

V

values (Fred2.Core.Result.AResult attribute) (Fred2.Core.Result.CleavageFragmentPredictionResult attribute) (Fred2.Core.Result.CleavageSitePredictionResult attribute) (Fred2.Core.Result.Distance2SelfResult attribute) (Fred2.Core.Result.EpitopePredictionResult attribute) (Fred2.Core.Result.TAPPredictionResult attribute) var() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method) Variant (class in Fred2.Core.Variant) (module)

VariationType (in module Fred2.Core.Variant) version (Fred2.CleavagePrediction.External.AExternalCleavageSitePrediction attribute) (Fred2.CleavagePrediction.External.NetChop_3_1 attribute) (Fred2.CleavagePrediction.PSSM.APSSMCleavageFragmentPredictor attribute) (Fred2.CleavagePrediction.PSSM.APSSMCleavageSitePredictor attribute) (Fred2.CleavagePrediction.PSSM.PCM attribute) (Fred2.CleavagePrediction.PSSM.PSSMGinodi attribute) (Fred2.CleavagePrediction.PSSM.ProteaSMMConsecutive attribute) (Fred2.CleavagePrediction.PSSM.ProteaSMMImmuno attribute) (Fred2.Core.Base.ACleavageFragmentPrediction attribute) (Fred2.Core.Base.ACleavageSitePrediction attribute) (Fred2.Core.Base.AEpitopePrediction attribute) (Fred2.Core.Base.AHLATyping attribute) (Fred2.Core.Base.ATAPPrediction attribute) (Fred2.EpitopePrediction.External.AExternalEpitopePrediction attribute) (Fred2.EpitopePrediction.External.NetCTLpan_1_1 attribute) (Fred2.EpitopePrediction.External.NetMHCII_2_2 attribute) (Fred2.EpitopePrediction.External.NetMHCIIpan_3_0 attribute) (Fred2.EpitopePrediction.External.NetMHCIIpan_3_1 attribute) (Fred2.EpitopePrediction.External.NetMHC_3_0 attribute) (Fred2.EpitopePrediction.External.NetMHC_3_4 attribute) (Fred2.EpitopePrediction.External.NetMHCpan_2_4 attribute) (Fred2.EpitopePrediction.External.NetMHCpan_2_8 attribute) (Fred2.EpitopePrediction.External.PickPocket_1_1 attribute) (Fred2.EpitopePrediction.PSSM.APSSMEpitopePrediction attribute) (Fred2.EpitopePrediction.PSSM.ARB attribute) (Fred2.EpitopePrediction.PSSM.BIMAS attribute) (Fred2.EpitopePrediction.PSSM.ComblibSidney2008 attribute) (Fred2.EpitopePrediction.PSSM.Epidemix attribute) (Fred2.EpitopePrediction.PSSM.Hammer attribute) (Fred2.EpitopePrediction.PSSM.SMM attribute) (Fred2.EpitopePrediction.PSSM.SMMPMBEC attribute) (Fred2.EpitopePrediction.PSSM.Syfpeithi attribute) (Fred2.EpitopePrediction.PSSM.TEPITOPEpan attribute) (Fred2.EpitopePrediction.SVM.ASVMEpitopePrediction attribute) (Fred2.EpitopePrediction.SVM.SVMHC attribute) (Fred2.EpitopePrediction.SVM.UniTope attribute) (Fred2.HLAtyping.External.AExternalHLATyping attribute) (Fred2.HLAtyping.External.ATHLATES_1_0 attribute) (Fred2.HLAtyping.External.OptiType_1_0 attribute) (Fred2.HLAtyping.External.Polysolver attribute) (Fred2.HLAtyping.External.Seq2HLA_2_2 attribute) (Fred2.TAPPrediction.PSSM.APSSMTAPPrediction attribute) (Fred2.TAPPrediction.PSSM.SMMTAP attribute) (Fred2.TAPPrediction.PSSM.TAPDoytchinova attribute) (Fred2.TAPPrediction.SVM.ASVMTAPPrediction attribute) (Fred2.TAPPrediction.SVM.SVMTAP attribute)

W

where() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method)

write_seqs() (Fred2.IO.UniProtAdapter.UniProtDB method)

X

xs() (Fred2.Core.Result.AResult method) (Fred2.Core.Result.CleavageFragmentPredictionResult method) (Fred2.Core.Result.CleavageSitePredictionResult method) (Fred2.Core.Result.Distance2SelfResult method) (Fred2.Core.Result.EpitopePredictionResult method) (Fred2.Core.Result.TAPPredictionResult method)