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.
FeaturesFeatures for immunogenicity prediction.
Features_ExtractFeaturesExtract features from a list of dataframes.
Features_ImportanceFeature selection based on their importances.
Features_IOFeature dataframes In/Out.
Features_MinimumFeaturesThe minimum set of the most important features.
Features_PreprocessingPreprocess peptide feature dataframes for machine learning.
ImmunogenicityImmunogenicity score.
NeighborNetworkNeighbor network analysis.
NeighborNetwork_ClusteringNeighbor network clustering analysis.
RepitopeRepitope: Epitope immunogenicity prediction via TCR-peptide...
TCRAffinitySingle TCR-peptide contact potential profiling.
Utility_ClassifierUtility functions for creating diagnostic plots for binary...
Utility_DFUtility functions for data frames.
Utility_ParCorParallelized correlation matrix calculation.
Utility_SequenceUtility functions for sequence analysis.
Utility_VennDiagramA utility function for creating a Venn diagram.
masato-ogishi/Repitope documentation built on Oct. 9, 2018, 7 a.m.