Files in richelbilderbeek/bbbq

The Bilderbeek Bianchi and Bogaart Question

NEWS.md R/are_detected.R R/bbbq.R R/calc_p_det_tmh_mut.R R/calculate-overlap-controls.R R/calculate-overlap.R R/check_haplotype.R R/check_ic50_prediction_tool.R R/check_ic50_prediction_tool_installation.R R/check_mhc_haplotype_name.R R/check_protein_sequences_length.R R/check_proteome_type.R R/check_target_name.R R/check_topology_prediction_tool.R R/convert_triplet_to_amino_acid.R R/correlate-to-hydrophobicity.R R/create_consensus_topology_conservation.R R/create_haplotypes_lut.R R/create_msa.R R/create_n_mers.R R/create_n_mers_tibble.R R/create_proteins_lut.R R/create_random_extreme_peptide.R R/create_random_hydrophobic_peptide.R R/create_random_peptide_with_hydrophobicity.R R/create_random_polypeptides.R R/create_random_tmh.R R/default_params_doc.R R/download_bergseng_et_al_2015_sup_1.R R/download_ic50s_lut.R R/get-protein-lengths.R R/get_aa_transition_matrix.R R/get_adjacent_sequences.R R/get_bbbq_theme.R R/get_bergseng_et_al_2015_sup_1.R R/get_bergseng_et_al_2015_sup_1_epitope_sequences.R R/get_bergseng_et_al_2015_sup_1_url.R R/get_covid_proteome_filename.R R/get_genetic_code.R R/get_hlas.R R/get_ic50_percentile_binder.R R/get_ic50_threshold.R R/get_ic50s_lut.R R/get_mhc1_allele_names.R R/get_mhc1_peptide_length.R R/get_mhc2_allele_names.R R/get_mhc2_haplotype_occurance.R R/get_mhc2_peptide_length.R R/get_mhc_allele_names.R R/get_mhc_peptide_length.R R/get_non_tmh_peptides_from_elution.R R/get_proteome.R R/get_proteome_filename.R R/get_target_english_name.R R/get_target_names.R R/get_test_covid_proteome_filename.R R/get_test_human_proteome_filename.R R/get_test_myco_proteome_filename.R R/get_test_proteome_filename.R R/get_tmh_lengths.R R/get_tmh_polypeptides_from_elution.R R/get_topology.R R/get_topology_filename.R R/get_transition_rate.R R/get_transition_rates.R R/get_uniprot_id.R R/hyPref.R R/hydrophobe-controls.R R/hydrophobicity-distribution-elution-data.R R/hydrophobicity-distribution.R R/is_detected.R R/is_polypeptide.R R/predict-binders.R R/predict_counts.R R/predict_counts_per_proteome.R R/predict_ic50s.R R/predict_n_coincidence_tmh_peptide.R R/prepare-data.R R/replace_nth_char.R R/simplify_haplotype_names.R R/tools.R R/utils-pipe.R README.md install.Rmd man/are_detected.Rd man/bbbq.Rd man/calc_p_det_tmh_mut.Rd man/calculate_overlap.Rd man/check_haplotype.Rd man/check_ic50_prediction_tool.Rd man/check_ic50_prediction_tool_installation.Rd man/check_mhc_haplotype_name.Rd man/check_protein_sequences_length.Rd man/check_proteome_type.Rd man/check_target_name.Rd man/check_topology_prediction_tool.Rd man/convert_triplet_to_amino_acid.Rd man/correlate_to_hydrophobicity.Rd man/create_consensus_topology_conservation.Rd man/create_haplotypes_lut.Rd man/create_msa.Rd man/create_n_mers.Rd man/create_n_mers_tibble.Rd man/create_proteins_lut.Rd man/create_random_extreme_peptide.Rd man/create_random_hydrophobic_peptide.Rd man/create_random_peptide_with_hydrophobicity.Rd man/create_random_peptides.Rd man/create_random_tmh.Rd man/default_params_doc.Rd man/download_bergseng_et_al_2015_sup_1.Rd man/download_ic50s_lut.Rd man/explode.Rd man/get_aa_transition_matrix.Rd man/get_adjacent_sequences.Rd man/get_bbbq_theme.Rd man/get_bergseng_et_al_2015_sup_1.Rd man/get_bergseng_et_al_2015_sup_1_epitope_sequences.Rd man/get_bergseng_et_al_2015_sup_1_url.Rd man/get_covid_proteome_filename.Rd man/get_genetic_code.Rd man/get_hlas.Rd man/get_ic50_percentile_binder.Rd man/get_ic50_threshold.Rd man/get_ic50s_lut.Rd man/get_mhc1_allele_names.Rd man/get_mhc1_haplotypes.Rd man/get_mhc1_peptide_length.Rd man/get_mhc2_allele_names.Rd man/get_mhc2_haplotype_occurance.Rd man/get_mhc2_haplotypes.Rd man/get_mhc2_peptide_length.Rd man/get_mhc_allele_names.Rd man/get_mhc_haplotypes.Rd man/get_mhc_peptide_length.Rd man/get_non_tmh_peptides_from_elution.Rd man/get_protein_lengths.Rd man/get_proteome.Rd man/get_proteome_filename.Rd man/get_target_english_name.Rd man/get_target_names.Rd man/get_test_covid_proteome_filename.Rd man/get_test_human_proteome_filename.Rd man/get_test_myco_proteome_filename.Rd man/get_test_proteome_filename.Rd man/get_tmh_lengths.Rd man/get_tmh_peptides_from_elution.Rd man/get_topology.Rd man/get_topology_filename.Rd man/get_transition_rate.Rd man/get_transition_rates.Rd man/get_uniprot_id.Rd man/hyPref.Rd man/hydrophobe_controls.Rd man/hydrophobe_overlap_controls.Rd man/hydrophobicity_distribution.Rd man/hydrophobicity_distribution_elution_data.Rd man/is_detected.Rd man/is_peptide.Rd man/nlapply.Rd man/pipe.Rd man/predict_binders.Rd man/predict_counts.Rd man/predict_counts_per_proteome.Rd man/predict_ic50s.Rd man/predict_n_coincidence_tmh_peptide.Rd man/prepare_data.Rd man/replace_nth_char.Rd man/simplify_haplotype_names.Rd scripts/create_non_human_topologies.R scripts/create_pureseqtm_topologies_without_selenoproteins.R tests/testthat.R tests/testthat/predict_n_binders_tmh.R tests/testthat/test-are_detected.R tests/testthat/test-calc_p_det_tmh_mut.R tests/testthat/test-calculate_overlap.R tests/testthat/test-check_haplotype.R tests/testthat/test-check_ic50_prediction_tool.R tests/testthat/test-check_ic50_prediction_tool_installation.R tests/testthat/test-check_mhc_haplotype_name.R tests/testthat/test-check_protein_sequences_length.R tests/testthat/test-check_proteome_type.R tests/testthat/test-check_target_name.R tests/testthat/test-check_topology_prediction_tool.R tests/testthat/test-convert_triplet_to_amino_acid.R tests/testthat/test-correlate_to_hydrophobicity.R tests/testthat/test-create_consensus_topology_conservation.R tests/testthat/test-create_haplotypes_lut.R tests/testthat/test-create_msa.R tests/testthat/test-create_n_mers.R tests/testthat/test-create_n_mers_tibble.R tests/testthat/test-create_proteins_lut.R tests/testthat/test-create_random_extreme_polypeptide.R tests/testthat/test-create_random_polypeptide_with_hydrophobicity.R tests/testthat/test-create_random_polypeptides.R tests/testthat/test-create_random_tmh.R tests/testthat/test-download_bergseng_et_al_2015_sup_1.R tests/testthat/test-download_ic50s_lut.R tests/testthat/test-get_aa_transition_matrix.R tests/testthat/test-get_adjacent_sequences.R tests/testthat/test-get_bbbq_theme.R tests/testthat/test-get_bergseng_et_al_2015_sup_1.R tests/testthat/test-get_bergseng_et_al_2015_sup_1_epitope_sequences.R tests/testthat/test-get_bergseng_et_al_2015_sup_1_url.R tests/testthat/test-get_covid_proteome_filename.R tests/testthat/test-get_genetic_code.R tests/testthat/test-get_hlas.R tests/testthat/test-get_ic50_percetile_binder.R tests/testthat/test-get_ic50_threshold.R tests/testthat/test-get_ic50s_lut.R tests/testthat/test-get_mhc1_allele_names.R tests/testthat/test-get_mhc1_peptide_length.R tests/testthat/test-get_mhc2_allele_names.R tests/testthat/test-get_mhc2_peptide_length.R tests/testthat/test-get_mhc_allele_names.R tests/testthat/test-get_mhc_peptide_length.R tests/testthat/test-get_non_tmh_polypeptides_from_elution.R tests/testthat/test-get_proteome.R tests/testthat/test-get_proteome_filename.R tests/testthat/test-get_target_english_name.R tests/testthat/test-get_target_names.R tests/testthat/test-get_test_covid_proteome_filename.R tests/testthat/test-get_test_proteome_filename.R tests/testthat/test-get_tmh_lengths.R tests/testthat/test-get_tmh_polypeptides_from_elution.R tests/testthat/test-get_topology.R tests/testthat/test-get_topology_filename.R tests/testthat/test-get_transition_rate.R tests/testthat/test-get_transition_rates.R tests/testthat/test-get_uniprot_id.R tests/testthat/test-hyPref.R tests/testthat/test-hydrophobicity_distribution_elution_data.R tests/testthat/test-is_detected.R tests/testthat/test-is_polypeptide.R tests/testthat/test-predict_counts.R tests/testthat/test-predict_counts_per_proteome.R tests/testthat/test-predict_ic50s.R tests/testthat/test-predict_n_coincidence_tmh_peptide.R tests/testthat/test-prepare_data.R tests/testthat/test-replace_nth_char.R tests/testthat/test-simplify_haplotype_names.R tests/testthat/test-to_mhcnuggets_name.R