Man pages for richelbilderbeek/bbbq
The Bilderbeek Bianchi and Bogaart Question
| are_detected | Are the protein sequences detected by either MHC-I or MHC-II? |
| bbbq | bbbq: The Bilderbeek Bianchi and Bogaart Question |
| calc_p_det_tmh_mut | Calculate the chance that a TMH one-mutation mutant is... |
| calculate_overlap | Determines the overlap of predicted HLA binders with... |
| check_haplotype | Check the haplotype |
| check_ic50_prediction_tool | Check the name of the IC50 prediction tool |
| check_ic50_prediction_tool_installation | Check the installation of the IC50 prediction tool |
| check_mhc_haplotype_name | Check an MHC haplotype name |
| check_protein_sequences_length | If if the protein sequences are long enough |
| check_proteome_type | Check if a 'proteome_type' is valid |
| check_target_name | Check if the target name is valid |
| check_topology_prediction_tool | Check the name of the topology prediction tool |
| convert_triplet_to_amino_acid | Convert a (DNA) triplet to the corresponding amino acid |
| correlate_to_hydrophobicity | Correlate to hydrophobicity |
| create_consensus_topology_conservation | Create a consensus-topology-conservation table |
| create_haplotypes_lut | Create a lookup table for haplotypes, MHC class and haplotype... |
| create_msa | Creata a multiple-sequence alignment |
| create_n_mers | Create the n-mers from a character string |
| create_n_mers_tibble | Create the n-mers from one or more character strings |
| create_proteins_lut | Create a protein lookup table from a proteome |
| create_random_extreme_peptide | Create a random peptide likelier to have an extreme... |
| create_random_hydrophobic_peptide | Create a random hydrophobic peptide |
| create_random_peptides | Create a random peptide |
| create_random_peptide_with_hydrophobicity | Creates a random peptide of a certain hydrophobicity |
| create_random_tmh | Create a random TMH sequences |
| default_params_doc | This function does nothing. It is intended to inherit is... |
| download_bergseng_et_al_2015_sup_1 | Downloads the XLSX file by Bergseng et al., 2015 |
| download_ic50s_lut | Download a lookup table for IC50 predictions of epitopes |
| explode | Explodes a string into a character vector |
| get_aa_transition_matrix | Get an amino acid transition matrix |
| get_adjacent_sequences | Get the adjacent sequences |
| get_bbbq_theme | Get the theme of the plots |
| get_bergseng_et_al_2015_sup_1 | Get the table of Supplementary Material 1 from Bergseng et... |
| get_bergseng_et_al_2015_sup_1_epitope_sequences | HIERO Get the table of Supplementary Material 1 from Bergseng... |
| get_bergseng_et_al_2015_sup_1_url | Get the URL for Bergseng et al., 2015 |
| get_covid_proteome_filename | Get the filename of the COVID-19 reference proteome |
| get_genetic_code | Get the genetic code |
| get_hlas | Get the MHC-I HLAs Copied from 'calculate_overlap' |
| get_ic50_percentile_binder | Get the IC50 percentile for which a peptide is a binder |
| get_ic50s_lut | Get a lookup table for IC50 predictions of epitopes |
| get_ic50_threshold | Get the threshold IC50 value |
| get_mhc1_allele_names | Get the MHC-I allele names used in this study. Use the... |
| get_mhc1_haplotypes | Deprecated function to the MHC-I allele names used in this... |
| get_mhc1_peptide_length | Get the peptide length used in MHC-I epitope predictions |
| get_mhc2_allele_names | Get the MHC-II allele names used in this study |
| get_mhc2_haplotype_occurance | Get the MHC-II haplotype occurance |
| get_mhc2_haplotypes | Deprecated function to get the MHC-II allele names used in... |
| get_mhc2_peptide_length | Get the peptide length used in MHC-II epitope predictions |
| get_mhc_allele_names | Get the MHC allele names used in this study. Use the official... |
| get_mhc_haplotypes | Deprecated function to het the MHC allele names used in this... |
| get_mhc_peptide_length | Get the MHC peptide length for a specific MHC class |
| get_non_tmh_peptides_from_elution | Get the TMH peptides from elution study |
| get_protein_lengths | Determines the lengths of all proteins in the human proteome. |
| get_proteome | Get a proteome as a tibble. |
| get_proteome_filename | Get the name of a proteome file |
| get_target_english_name | Get the English description of a target |
| get_target_names | Get all the target names |
| get_test_covid_proteome_filename | Get the filename of a test SARS-CoV-2 reference proteome |
| get_test_human_proteome_filename | Get the filename of a test Homo Sapiens reference proteome |
| get_test_myco_proteome_filename | Get the filename of a test Mycobacterium reference proteome |
| get_test_proteome_filename | Get the filename of a testing proteome |
| get_tmh_lengths | Get the lengths of the TMHs |
| get_tmh_peptides_from_elution | Get the TMH peptides from elution study |
| get_topology | Get a topology as a tibble. |
| get_topology_filename | Get the name of a topology file |
| get_transition_rate | Get the AA transition rate from the FLU transition rate... |
| get_transition_rates | Get the transition rates from the one focal protein sequence... |
| get_uniprot_id | Get the Uniprot ID from a target |
| hydrophobe_controls | Generates a set of 9mers that do not overlap with... |
| hydrophobe_overlap_controls | Performs the same analysis as "calculate-overlap.R", but now... |
| hydrophobicity_distribution | Determines the hydrophobicity distribution of all peptides in... |
| hydrophobicity_distribution_elution_data | Creates figures 4a and 4b |
| hyPref | Does something |
| is_detected | Determine if the haplotype has at least one binder to the... |
| is_peptide | Determine if the AA sequence is a peptide |
| nlapply | Version of lapply that also passes along the name of each... |
| pipe | Pipe operator |
| predict_binders | Predict binders |
| predict_counts | Predict counts of one protein and one haplotype |
| predict_counts_per_proteome | Predict counts of one or more proteins and one haplotype |
| predict_ic50s | Predict IC50s |
| predict_n_coincidence_tmh_peptide | Predict the number of n-mers and the number of n-mers that... |
| prepare_data | Converts the human proteome, as downloaded from UniProt, into... |
| replace_nth_char | Replace the nth char of a string |
| simplify_haplotype_names | Simplify haplotype names to numbers Will be NA for unknown... |
