polyclonal package¶
polyclonal¶
Package for modeling mutational escape from polyclonal antibodies using deep mutational scanning experiments.
Importing this package imports the following objects into the package namespace:
It also imports the following alphabets:
Submodules¶
- alphabets
AASAAS_WITHGAPAAS_WITHSTOPAAS_WITHSTOP_WITHGAPbiochem_order_aas()- pdb_utils
extract_atom_locations()inter_residue_distances()reassign_b_factor()- plot
DEFAULT_NEGATIVE_COLORDEFAULT_POSITIVE_COLORSTAB10_COLORS_NOGRAYactivity_wt_barplot()color_gradient_hex()corr_heatmap()curves_plot()lineplot_and_heatmap()- polyclonal
PolyclonalPolyclonal.epitopesPolyclonal.mutationsPolyclonal.alphabetPolyclonal.sitesPolyclonal.sequential_integer_sitesPolyclonal.wtsPolyclonal.epitope_colorsPolyclonal.data_to_fitPolyclonal.spatial_distancesPolyclonal.mutations_times_seenPolyclonal.distance_matrixPolyclonal.DEFAULT_SCIPY_MINIMIZE_KWARGSPolyclonal.activity_wt_barplot()Polyclonal.activity_wt_dfPolyclonal.curve_specs_dfPolyclonal.curves_plot()Polyclonal.epitope_harmonized_model()Polyclonal.filter_variants_by_seen_muts()Polyclonal.fit()Polyclonal.hill_coefficient_dfPolyclonal.icXX()Polyclonal.mut_escape_corr()Polyclonal.mut_escape_dfPolyclonal.mut_escape_pdb_b_factor()Polyclonal.mut_escape_plot()Polyclonal.mut_escape_site_summary_df()Polyclonal.mut_icXX_df()Polyclonal.mut_icXX_plot()Polyclonal.non_neutralized_frac_dfPolyclonal.prob_escape()Polyclonal.site_level_model()
PolyclonalConcentrationErrorPolyclonalFitErrorPolyclonalHarmonizeError- polyclonal_collection
PolyclonalAveragePolyclonalBootstrapPolyclonalCollectionPolyclonalCollection.modelsPolyclonalCollection.model_descriptorsPolyclonalCollection.descriptor_namesPolyclonalCollection.unique_descriptor_namesPolyclonalCollection.epitopesPolyclonalCollection.epitope_colorsPolyclonalCollection.alphabetPolyclonalCollection.sequential_integer_sitesPolyclonalCollection.sitesPolyclonalCollection.default_avg_to_plotPolyclonalCollection.regionsPolyclonalCollection.n_models_by_sitePolyclonalCollection.activity_wt_barplot()PolyclonalCollection.activity_wt_dfPolyclonalCollection.activity_wt_df_replicatesPolyclonalCollection.curve_specs_dfPolyclonalCollection.curve_specs_df_replicatesPolyclonalCollection.curves_plot()PolyclonalCollection.hill_coefficient_dfPolyclonalCollection.hill_coefficient_df_replicatesPolyclonalCollection.icXX()PolyclonalCollection.icXX_replicates()PolyclonalCollection.mut_escape_corr()PolyclonalCollection.mut_escape_corr_heatmap()PolyclonalCollection.mut_escape_dfPolyclonalCollection.mut_escape_df_replicatesPolyclonalCollection.mut_escape_df_w_model_valuesPolyclonalCollection.mut_escape_plot()PolyclonalCollection.mut_escape_site_summary_df()PolyclonalCollection.mut_escape_site_summary_df_replicates()PolyclonalCollection.mut_icXX_df()PolyclonalCollection.mut_icXX_df_replicates()PolyclonalCollection.mut_icXX_df_w_model_values()PolyclonalCollection.mut_icXX_plot()PolyclonalCollection.non_neutralized_frac_dfPolyclonalCollection.non_neutralized_frac_df_replicatesPolyclonalCollection.prob_escape()PolyclonalCollection.prob_escape_replicates()
PolyclonalCollectionFitErrorcreate_bootstrap_sample()fit_models()- utils
MutationParsershift_mut_site()site_level_variants()tidy_to_corr()
