Man pages for masato-ogishi/Repitope
Epitope immunogenicity prediction through in silico TCR-peptide contact potential profiling

ContactPotentialProfiling_AACPMatrixAmino acid pairwise contact potential (AACP) matrix.
ContactPotentialProfiling_FragmentLibraryGenerate sequence fragment libraries.
DataPreparation_EpitopeDatasetCompile epitope datasets retrieved from IEDB and other...
DataPreparation_NetMHCUtility functions for NetMHC.
DataPreparation_TCR_FastQDumpDownloading fastQ files from NCBI Sequence Read Archive...
DataPreparation_TCR_MiXCRMiXCR workflow.
Dataset_EpitopeDatasetCompiled datasets of MHC class I and class II epitopes and...
Dataset_TCRDatasetsA compiled dataset of human TCR beta CDR3 sequences
Dataset_TCRPeptidePairDatasetA compiled dataset of human TCR-peptide pairs.
EpitopePrioritizationEpitope prioritization based on immunogenicity scores and...
FeaturesFeature computation.
Features_ExtractFeaturesExtract features from a list of feature dataframes.
Features_ImportanceImportance-based feature selection.
Features_IOImporting and exporting utilities for feature dataframes.
Features_MinimumFeaturesThe minimum set of the most important features.
Features_PreprocessingFeature preprocessing.
ImmunogenicityImmunogenicity score.
NeighborNetworkNeighbor network analysis.
NeighborNetwork_ClusteringNeighbor network clustering analysis.
RepitopeRepitope: Epitope immunogenicity prediction via TCR-peptide...
SingleTCRAnalysisSingle TCR-peptide contact potential profiling.
Utility_ClassifierUtility functions for creating diagnostic plots for binary...
Utility_DFUtility functions for data frames.
Utility_FastUniqueThe fastest "unique" function.
Utility_ParCorParallelized correlation matrix computation.
Utility_SequenceUtility functions for sequence analysis.
Utility_VennDiagramVenn diagram.
masato-ogishi/Repitope documentation built on Feb. 14, 2023, 5:47 a.m.