Man pages for masato-ogishi/Repitope
Epitope immunogenicity prediction through in silico TCR-peptide contact potential profiling
| ContactPotentialProfiling_AACPMatrix | Amino acid pairwise contact potential (AACP) matrix. |
| ContactPotentialProfiling_FragmentLibrary | Generate sequence fragment libraries. |
| DataPreparation_EpitopeDataset | Compile epitope datasets retrieved from IEDB and other... |
| DataPreparation_NetMHC | Utility functions for NetMHC. |
| DataPreparation_TCR_FastQDump | Downloading fastQ files from NCBI Sequence Read Archive... |
| DataPreparation_TCR_MiXCR | MiXCR workflow. |
| Dataset_EpitopeDataset | Compiled datasets of MHC class I and class II epitopes and... |
| Dataset_TCRDatasets | A compiled dataset of human TCR beta CDR3 sequences |
| Dataset_TCRPeptidePairDataset | A compiled dataset of human TCR-peptide pairs. |
| EpitopePrioritization | Epitope prioritization based on immunogenicity scores and... |
| Features | Feature computation. |
| Features_ExtractFeatures | Extract features from a list of feature dataframes. |
| Features_Importance | Importance-based feature selection. |
| Features_IO | Importing and exporting utilities for feature dataframes. |
| Features_MinimumFeatures | The minimum set of the most important features. |
| Features_Preprocessing | Feature preprocessing. |
| Immunogenicity | Immunogenicity score. |
| NeighborNetwork | Neighbor network analysis. |
| NeighborNetwork_Clustering | Neighbor network clustering analysis. |
| Repitope | Repitope: Epitope immunogenicity prediction via TCR-peptide... |
| SingleTCRAnalysis | Single TCR-peptide contact potential profiling. |
| Utility_Classifier | Utility functions for creating diagnostic plots for binary... |
| Utility_DF | Utility functions for data frames. |
| Utility_FastUnique | The fastest "unique" function. |
| Utility_ParCor | Parallelized correlation matrix computation. |
| Utility_Sequence | Utility functions for sequence analysis. |
| Utility_VennDiagram | Venn diagram. |
