Man pages for fcampelo/epitopes
Processing and Feature Extraction for Epitope Data
| calc_features | Calculate statistical and physicochemical features for... |
| calc_performance | Calculate epitope classification performance indices |
| filter_epitopes | Filter epitopes by taxonomy and host |
| fit_model | Fit Random Forest model to epitope data |
| get_feature_functions | Print available feature calculation functions |
| get_IEDB | Download and unzip IEDB database (XML export) |
| get_LBCE | Extract linear B Cell epitopes from XML files retrieved from... |
| get_proteins | Retrieve protein sequences and data from GenBank and Uniprot |
| get_taxonomy | Retrieve taxonomic classification tables from NCBI. |
| label_proteins | Label protein positions based on epitope data |
| make_heterogeneous_dataset | Build a heterogeneou dataset of predefined size |
| make_OrgSpec_datasets | Build organism-specific data sets for training epitope... |
| make_proteins_dataset | Builds a partially labelled dataset from protein and epitope... |
| make_window_df | Assemble a sliding window representation of epitope or... |
| prepare_join_df | Merge and filter epitope and protein data |
| read_abcpred | Read saved output from ABCPred |
| read_bepipred2 | Read saved output from Bepipred2 |
| read_ibceel | Read saved output from iBCE-EL |
| read_lbtope | Read saved output from LBtope |
| read_svmtrip | Read saved output from SVMtrip |
| smooth_predictions | Smoothing of prediction vectors |
| split_epitope_data | Split epitope data based on epitope, protein or organism IDs. |
