├── .gitattributes ├── .gitignore ├── .rsync_exclude ├── LICENSE ├── README.md ├── Snakefile ├── bin ├── analysis │ ├── 0_data │ │ ├── check_normalisation.R │ │ ├── clinvar_classification.R │ │ ├── data_summary_plots.R │ │ ├── gene_repeats.R │ │ ├── sift_correlation.R │ │ ├── summarise_standardised_data.R │ │ ├── summarise_studies.py │ │ ├── validate_araya_2012_yap1.R │ │ ├── validate_dorrity_2018_ste12.R │ │ ├── validate_giacomelli_2018_tp53.R │ │ ├── validate_heredia_2018.R │ │ ├── validate_kitzman_2015_gal4.R │ │ ├── validate_melnikov_2014_aph3ii.R │ │ ├── validate_sarkisyan_2016_gfp.R │ │ └── validate_starita_2013_ube4b.R │ ├── 1_landscape │ │ ├── dimensionality_reduction.R │ │ ├── mutation_types.R │ │ └── project_landscape.py │ ├── 2_subtypes │ │ ├── all_positions.R │ │ ├── characterise_subtypes.R │ │ ├── cluster_assignment.R │ │ ├── compare_hclust_dynamic_deep_split.R │ │ ├── compare_subtypes.R │ │ ├── estimate_number.R │ │ ├── evaluate_kmeans_k.R │ │ ├── final_subtypes.R │ │ ├── make_subtypes.R │ │ ├── sequence_context.R │ │ ├── sift_subtypes.R │ │ └── subtypes_clinvar.R │ └── 3_continuous │ │ └── all_position_characterisation.R ├── data_processing │ ├── combine_standardised_data.R │ ├── filter_pdb.py │ ├── foldx_combine.py │ ├── foldx_variants.py │ ├── get_backbone_angles.py │ ├── get_chem_env_profiles.py │ ├── make_gene_fasta.py │ └── standardise_study_template.R ├── figures │ ├── figure1.R │ ├── figure2.R │ ├── figure3.R │ ├── figure3_thesis.R │ ├── figure4.R │ ├── figure4_thesis.R │ ├── figure5.R │ ├── figure6.R │ ├── figureS1.R │ ├── figureS2.R │ ├── figureS28.R │ ├── figureS29.R │ ├── figureS3.R │ ├── figureS4.R │ ├── figureS5.R │ ├── figureS6.R │ ├── figureS7.R │ └── figureS8_27.R ├── pipeline │ ├── data_validation.smk │ ├── figures.smk │ ├── foldx.smk │ ├── landscape.smk │ ├── sequence_statistics.smk │ ├── standardisation.smk │ ├── structure_statistics.smk │ └── subtypes.smk └── utils │ ├── farm_sync.sh │ ├── setup_study_folder.sh │ └── validate_study_yaml.py ├── cluster.yaml ├── data ├── combined_mutational_scans.tsv ├── long_combined_mutational_scans.tsv ├── pdb │ ├── README.md │ ├── adrb2.pdb │ ├── amie.pdb │ ├── aph3ii.pdb │ ├── braf.pdb │ ├── brca1.pdb │ ├── calm1.pdb │ ├── cbs.pdb │ ├── ccr5.pdb │ ├── cp.pdb │ ├── cxcr4.pdb │ ├── dbr1.pdb │ ├── gal4.pdb │ ├── gfp.pdb │ ├── ha.pdb │ ├── hsp90.pdb │ ├── infa.pdb │ ├── mapk1.pdb │ ├── np.pdb │ ├── pab1.pdb │ ├── proteing.pdb │ ├── pten.pdb │ ├── ras.pdb │ ├── src.pdb │ ├── ste12.pdb │ ├── sumo1.pdb │ ├── tdp43.pdb │ ├── tem1.pdb │ ├── tp53.pdb │ ├── tpk1.pdb │ ├── tpmt.pdb │ ├── ube2i.pdb │ ├── ube4b.pdb │ ├── ubi.pdb │ └── yap1.pdb ├── studies │ ├── ahler_2019_src │ │ ├── ahler_2019_src.yaml │ │ └── standardise_ahler_2019_src.R │ ├── araya_2012_yap1 │ │ ├── araya_2012_yap1.yaml │ │ └── standardise_araya_2012_yap1.R │ ├── ashenberg_2017_np │ │ ├── ashenberg_2017_np.yaml │ │ └── standardise_ashenberg_2017_np.R │ ├── bandaru_2017_ras │ │ ├── bandaru_2017_ras.yaml │ │ └── standardise_bandaru_2017_ras.R │ ├── bolognesi_2019_tdp43 │ │ ├── bolognesi_2019_tdp43.yaml │ │ └── standardise_bolognesi_2019_tdp43.R │ ├── brenan_2016_mapk1 │ │ ├── brenan_2016_mapk1.yaml │ │ └── standardise_brenan_2016_mapk1.R │ ├── dorrity_2018_ste12 │ │ ├── dorrity_2018_ste12.yaml │ │ └── standardise_dorrity_2018_ste12.R │ ├── doud_2015_np │ │ ├── doud_2015_np.yaml │ │ └── standardise_doud_2015_np.R │ ├── findlay_2014_dbr1 │ │ ├── findlay_2014_dbr1.yaml │ │ └── standardise_findlay_2014_dbr1.R │ ├── findlay_2018_brca1 │ │ ├── findlay_2018_brca1.yaml │ │ └── standardise_findlay_2018_brca1.R │ ├── firnberg_2014_tem1 │ │ ├── firnberg_2014_tem1.yaml │ │ └── standardise_firnberg_2014_tem1.R │ ├── giacomelli_2018_tp53 │ │ ├── giacomelli_2018_tp53.yaml │ │ └── standardise_giacomelli_2018_tp53.R │ ├── hartman_2018_cp │ │ ├── hartman_2018_cp.yaml │ │ └── standardise_hartman_2018_cp.R │ ├── heredia_2018_ccr5 │ │ ├── heredia_2018_ccr5.yaml │ │ └── standardise_heredia_2018_ccr5.R │ ├── heredia_2018_cxcr4 │ │ ├── heredia_2018_cxcr4.yaml │ │ └── standardise_heredia_2018_cxcr4.R │ ├── hietpas_2011_hsp90 │ │ ├── hietpas_2011_hsp90.yaml │ │ └── standardise_hietpas_2011_hsp90.R │ ├── jiang_2013_hsp90 │ │ ├── jiang_2013_hsp90.yaml │ │ └── standardise_jiang_2013_hsp90.R │ ├── jones_2019_adrb2 │ │ ├── jones_2019_adrb2.yaml │ │ └── standardise_jones_2019_adrb2.R │ ├── kelsic_2016_infa │ │ ├── kelsic_2016_infa.yaml │ │ └── standardise_kelsic_2016_infa.R │ ├── kitzman_2015_gal4 │ │ ├── kitzman_2015_gal4.yaml │ │ └── standardise_kitzman_2015_gal4.R │ ├── lee_2018_ha │ │ ├── lee_2018_ha.yaml │ │ └── standardise_lee_2018_ha.R │ ├── matreyek_2018_pten │ │ ├── matreyek_2018_pten.yaml │ │ └── standardise_matreyek_2018_pten.R │ ├── matreyek_2018_tpmt │ │ ├── matreyek_2018_tpmt.yaml │ │ └── standardise_matreyek_2018_tpmt.R │ ├── melamed_2013_pab1 │ │ ├── melamed_2013_pab1.yaml │ │ └── standardise_melamed_2013_pab1.R │ ├── melnikov_2014_aph3ii │ │ ├── melnikov_2014_aph3ii.yaml │ │ └── standardise_melnikov_2014_aph3ii.R │ ├── mishra_2016_hsp90 │ │ ├── mishra_2016_hsp90.yaml │ │ └── standardise_mishra_2016_hsp90.R │ ├── olson_2014_proteing │ │ ├── olson_2014_proteing.yaml │ │ └── standardise_olson_2014_proteing.R │ ├── roscoe_2013_ubi │ │ ├── roscoe_2013_ubi.yaml │ │ └── standardise_roscoe_2013_ubi.R │ ├── roscoe_2014_ubi │ │ ├── roscoe_2014_ubi.yaml │ │ └── standardise_roscoe_2014_ubi.R │ ├── sarkisyan_2016_gfp │ │ ├── sarkisyan_2016_gfp.yaml │ │ └── standardise_sarkisyan_2016_gfp.R │ ├── starita_2013_ube4b │ │ ├── standardise_starita_2013_ube4b.R │ │ └── starita_2013_ube4b.yaml │ ├── starita_2015_brca1 │ │ ├── standardise_starita_2015_brca1.R │ │ └── starita_2015_brca1.yaml │ ├── steinberg_2016_tem1 │ │ ├── standardise_steinberg_2016_tem1.R │ │ └── steinberg_2016_tem1.yaml │ ├── sun_2018_cbs │ │ ├── standardise_sun_2018_cbs.R │ │ └── sun_2018_cbs.yaml │ ├── wagenaar_2014_braf │ │ ├── standardise_wagenaar_2014_braf.R │ │ └── wagenaar_2014_braf.yaml │ ├── weile_2017_calm1 │ │ ├── standardise_weile_2017_calm1.R │ │ └── weile_2017_calm1.yaml │ ├── weile_2017_sumo1 │ │ ├── standardise_weile_2017_sumo1.R │ │ └── weile_2017_sumo1.yaml │ ├── weile_2017_tpk1 │ │ ├── standardise_weile_2017_tpk1.R │ │ └── weile_2017_tpk1.yaml │ ├── weile_2017_ube2i │ │ ├── standardise_weile_2017_ube2i.R │ │ └── weile_2017_ube2i.yaml │ └── wrenbeck_2017_amie │ │ ├── standardise_wrenbeck_2017_amie.R │ │ └── wrenbeck_2017_amie.yaml └── subtypes │ ├── final_subtypes.tsv │ └── sift_scores.tsv ├── docs ├── combined_mutational_scans_readme.txt ├── foldx_eqn.md ├── subtype_descriptions.md └── subtypes_readme.txt ├── figures ├── 4_figures │ ├── parts │ │ └── arrow.png │ ├── position_examples │ │ ├── adrb2_ala_small_hydro.png │ │ ├── adrb2_domains.png │ │ ├── aph3ii_arg_not_proline.png │ │ ├── cbs_asp_ionic.png │ │ ├── cbs_phe_pi.png │ │ ├── ccr5_cys_aromatic.png │ │ ├── ccr5_cys_disulphide.png │ │ ├── ccr5_domains.png │ │ ├── cxcr4_domains.png │ │ ├── gal4_cys_zinc.png │ │ ├── np_cys_aromatic.png │ │ ├── pab1_arg_not_neg.png │ │ ├── ras_aliphatic_entropy.png │ │ ├── ras_met_buried.png │ │ ├── tem1_asp_ligand.png │ │ └── tem1_asp_sa.png │ └── proteins │ │ ├── adrb2.png │ │ ├── amie.png │ │ ├── aph3ii.png │ │ ├── brca1.png │ │ ├── calm1.png │ │ ├── cbs.png │ │ ├── ccr5.png │ │ ├── cp.png │ │ ├── cxcr4.png │ │ ├── dbr1.png │ │ ├── gal4.png │ │ ├── ha.png │ │ ├── hsp90.png │ │ ├── infa.png │ │ ├── np.png │ │ ├── pab1.png │ │ ├── proteing.png │ │ ├── pten.png │ │ ├── ras.png │ │ ├── src.png │ │ ├── ste12.png │ │ ├── sumo1.png │ │ ├── tem1.png │ │ ├── tp53.png │ │ ├── tpk1.png │ │ ├── tpmt.png │ │ ├── ube2i.png │ │ ├── ube4b.png │ │ ├── ubi.png │ │ └── yap1.png ├── 5_thesis │ └── figure1_1.svg └── summary.svg ├── meta ├── README.md ├── fasta │ ├── H3N2_A_Aichi_2_1968_np.fa │ ├── H3N2_A_Perth_16_2009_ha.fa │ ├── a_victoria_gfp.fa │ ├── b_subtilis_gdh.fa │ ├── bacteriophage_ms2_cp.fa │ ├── e_coli_aph3ii.fa │ ├── e_coli_ccdb.fa │ ├── e_coli_infa.fa │ ├── e_coli_tem1.fa │ ├── h_sapiens_adrb2.fa │ ├── h_sapiens_braf.fa │ ├── h_sapiens_brca1.fa │ ├── h_sapiens_calm1.fa │ ├── h_sapiens_cbs.fa │ ├── h_sapiens_ccr5.fa │ ├── h_sapiens_cxcr4.fa │ ├── h_sapiens_dbr1.fa │ ├── h_sapiens_mapk1.fa │ ├── h_sapiens_pten.fa │ ├── h_sapiens_ras.fa │ ├── h_sapiens_src.fa │ ├── h_sapiens_sumo1.fa │ ├── h_sapiens_tdp43.fa │ ├── h_sapiens_tp53.fa │ ├── h_sapiens_tpk1.fa │ ├── h_sapiens_tpmt.fa │ ├── h_sapiens_ube2i.fa │ ├── h_sapiens_yap1.fa │ ├── m_musculus_ube4b.fa │ ├── p_aeruginosa_amie.fa │ ├── s_cerevisiae_gal4.fa │ ├── s_cerevisiae_gcn4.fa │ ├── s_cerevisiae_hsc82.fa │ ├── s_cerevisiae_hsp90.fa │ ├── s_cerevisiae_pab1.fa │ ├── s_cerevisiae_ste12.fa │ ├── s_cerevisiae_ubi.fa │ ├── s_pyrogenes_cas9.fa │ ├── strep_protein_g_precursor.fa │ └── streptococcus_proteing.fa ├── final_subtypes.yaml ├── residue_hydrophobicity.tsv ├── structures.yaml ├── study_template.yaml ├── subtypes │ ├── gmm_pca.yaml │ ├── gmm_pca_no_sig.yaml │ ├── gmm_profile.yaml │ ├── hclust_pca_dynamic.yaml │ ├── hclust_pca_no_sig_dynamic.yaml │ ├── hclust_pca_no_sig_dynamic_cos_deep_0.yaml │ ├── hclust_pca_no_sig_dynamic_cos_deep_1.yaml │ ├── hclust_profile_dynamic.yaml │ ├── hclust_profile_dynamic_cos.yaml │ ├── hdbscan_pca.yaml │ ├── hdbscan_pca_no_sig.yaml │ ├── hdbscan_profile.yaml │ ├── kmeans_pca.yaml │ ├── kmeans_pca_no_sig.yaml │ ├── kmeans_profile.yaml │ ├── pam_pca_no_sig_cos.yaml │ ├── pam_pca_no_sig_man.yaml │ ├── pam_profile_cos.yaml │ └── pam_profile_man.yaml ├── uniprot_domains.gff └── uniprot_ptms.tsv ├── snakemake.yaml └── src ├── chemical_environment.py ├── colour_spectrum.py ├── config.R ├── continuous.R ├── dimensionality_reduction.R ├── pymol_utils.py ├── study_standardising.R ├── subtype_characterisation.R ├── subtype_clustering.R ├── subtypes_utils.R └── subtypes_utils.py /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/.gitattributes -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/.gitignore -------------------------------------------------------------------------------- /.rsync_exclude: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/.rsync_exclude -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/README.md -------------------------------------------------------------------------------- /Snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/Snakefile -------------------------------------------------------------------------------- /bin/analysis/0_data/check_normalisation.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/analysis/0_data/check_normalisation.R -------------------------------------------------------------------------------- /bin/analysis/0_data/clinvar_classification.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/analysis/0_data/clinvar_classification.R -------------------------------------------------------------------------------- /bin/analysis/0_data/data_summary_plots.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/analysis/0_data/data_summary_plots.R -------------------------------------------------------------------------------- /bin/analysis/0_data/gene_repeats.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/analysis/0_data/gene_repeats.R -------------------------------------------------------------------------------- /bin/analysis/0_data/sift_correlation.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/analysis/0_data/sift_correlation.R -------------------------------------------------------------------------------- /bin/analysis/0_data/summarise_standardised_data.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/analysis/0_data/summarise_standardised_data.R -------------------------------------------------------------------------------- /bin/analysis/0_data/summarise_studies.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/analysis/0_data/summarise_studies.py -------------------------------------------------------------------------------- /bin/analysis/0_data/validate_araya_2012_yap1.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/analysis/0_data/validate_araya_2012_yap1.R -------------------------------------------------------------------------------- /bin/analysis/0_data/validate_dorrity_2018_ste12.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/analysis/0_data/validate_dorrity_2018_ste12.R -------------------------------------------------------------------------------- /bin/analysis/0_data/validate_giacomelli_2018_tp53.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/analysis/0_data/validate_giacomelli_2018_tp53.R -------------------------------------------------------------------------------- /bin/analysis/0_data/validate_heredia_2018.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/analysis/0_data/validate_heredia_2018.R -------------------------------------------------------------------------------- /bin/analysis/0_data/validate_kitzman_2015_gal4.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/analysis/0_data/validate_kitzman_2015_gal4.R -------------------------------------------------------------------------------- /bin/analysis/0_data/validate_melnikov_2014_aph3ii.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/analysis/0_data/validate_melnikov_2014_aph3ii.R -------------------------------------------------------------------------------- /bin/analysis/0_data/validate_sarkisyan_2016_gfp.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/analysis/0_data/validate_sarkisyan_2016_gfp.R -------------------------------------------------------------------------------- /bin/analysis/0_data/validate_starita_2013_ube4b.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/analysis/0_data/validate_starita_2013_ube4b.R -------------------------------------------------------------------------------- /bin/analysis/1_landscape/dimensionality_reduction.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/analysis/1_landscape/dimensionality_reduction.R -------------------------------------------------------------------------------- /bin/analysis/1_landscape/mutation_types.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/analysis/1_landscape/mutation_types.R -------------------------------------------------------------------------------- /bin/analysis/1_landscape/project_landscape.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/analysis/1_landscape/project_landscape.py -------------------------------------------------------------------------------- /bin/analysis/2_subtypes/all_positions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/analysis/2_subtypes/all_positions.R -------------------------------------------------------------------------------- /bin/analysis/2_subtypes/characterise_subtypes.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/analysis/2_subtypes/characterise_subtypes.R -------------------------------------------------------------------------------- /bin/analysis/2_subtypes/cluster_assignment.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/analysis/2_subtypes/cluster_assignment.R -------------------------------------------------------------------------------- /bin/analysis/2_subtypes/compare_hclust_dynamic_deep_split.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/analysis/2_subtypes/compare_hclust_dynamic_deep_split.R -------------------------------------------------------------------------------- /bin/analysis/2_subtypes/compare_subtypes.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/analysis/2_subtypes/compare_subtypes.R -------------------------------------------------------------------------------- /bin/analysis/2_subtypes/estimate_number.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/analysis/2_subtypes/estimate_number.R -------------------------------------------------------------------------------- /bin/analysis/2_subtypes/evaluate_kmeans_k.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/analysis/2_subtypes/evaluate_kmeans_k.R -------------------------------------------------------------------------------- /bin/analysis/2_subtypes/final_subtypes.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/analysis/2_subtypes/final_subtypes.R -------------------------------------------------------------------------------- /bin/analysis/2_subtypes/make_subtypes.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/analysis/2_subtypes/make_subtypes.R -------------------------------------------------------------------------------- /bin/analysis/2_subtypes/sequence_context.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/analysis/2_subtypes/sequence_context.R -------------------------------------------------------------------------------- /bin/analysis/2_subtypes/sift_subtypes.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/analysis/2_subtypes/sift_subtypes.R -------------------------------------------------------------------------------- /bin/analysis/2_subtypes/subtypes_clinvar.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/analysis/2_subtypes/subtypes_clinvar.R -------------------------------------------------------------------------------- /bin/analysis/3_continuous/all_position_characterisation.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/analysis/3_continuous/all_position_characterisation.R -------------------------------------------------------------------------------- /bin/data_processing/combine_standardised_data.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/data_processing/combine_standardised_data.R -------------------------------------------------------------------------------- /bin/data_processing/filter_pdb.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/data_processing/filter_pdb.py -------------------------------------------------------------------------------- /bin/data_processing/foldx_combine.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/data_processing/foldx_combine.py -------------------------------------------------------------------------------- /bin/data_processing/foldx_variants.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/data_processing/foldx_variants.py -------------------------------------------------------------------------------- /bin/data_processing/get_backbone_angles.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/data_processing/get_backbone_angles.py -------------------------------------------------------------------------------- /bin/data_processing/get_chem_env_profiles.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/data_processing/get_chem_env_profiles.py -------------------------------------------------------------------------------- /bin/data_processing/make_gene_fasta.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/data_processing/make_gene_fasta.py -------------------------------------------------------------------------------- /bin/data_processing/standardise_study_template.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/data_processing/standardise_study_template.R -------------------------------------------------------------------------------- /bin/figures/figure1.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/figures/figure1.R -------------------------------------------------------------------------------- /bin/figures/figure2.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/figures/figure2.R -------------------------------------------------------------------------------- /bin/figures/figure3.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/figures/figure3.R -------------------------------------------------------------------------------- /bin/figures/figure3_thesis.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/figures/figure3_thesis.R -------------------------------------------------------------------------------- /bin/figures/figure4.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/figures/figure4.R -------------------------------------------------------------------------------- /bin/figures/figure4_thesis.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/figures/figure4_thesis.R -------------------------------------------------------------------------------- /bin/figures/figure5.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/figures/figure5.R -------------------------------------------------------------------------------- /bin/figures/figure6.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/figures/figure6.R -------------------------------------------------------------------------------- /bin/figures/figureS1.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/figures/figureS1.R -------------------------------------------------------------------------------- /bin/figures/figureS2.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/figures/figureS2.R -------------------------------------------------------------------------------- /bin/figures/figureS28.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/figures/figureS28.R -------------------------------------------------------------------------------- /bin/figures/figureS29.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/figures/figureS29.R -------------------------------------------------------------------------------- /bin/figures/figureS3.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/figures/figureS3.R -------------------------------------------------------------------------------- /bin/figures/figureS4.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/figures/figureS4.R -------------------------------------------------------------------------------- /bin/figures/figureS5.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/figures/figureS5.R -------------------------------------------------------------------------------- /bin/figures/figureS6.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/figures/figureS6.R -------------------------------------------------------------------------------- /bin/figures/figureS7.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/figures/figureS7.R -------------------------------------------------------------------------------- /bin/figures/figureS8_27.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/figures/figureS8_27.R -------------------------------------------------------------------------------- /bin/pipeline/data_validation.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/pipeline/data_validation.smk -------------------------------------------------------------------------------- /bin/pipeline/figures.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/pipeline/figures.smk -------------------------------------------------------------------------------- /bin/pipeline/foldx.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/pipeline/foldx.smk -------------------------------------------------------------------------------- /bin/pipeline/landscape.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/pipeline/landscape.smk -------------------------------------------------------------------------------- /bin/pipeline/sequence_statistics.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/pipeline/sequence_statistics.smk -------------------------------------------------------------------------------- /bin/pipeline/standardisation.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/pipeline/standardisation.smk -------------------------------------------------------------------------------- /bin/pipeline/structure_statistics.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/pipeline/structure_statistics.smk -------------------------------------------------------------------------------- /bin/pipeline/subtypes.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/pipeline/subtypes.smk -------------------------------------------------------------------------------- /bin/utils/farm_sync.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/utils/farm_sync.sh -------------------------------------------------------------------------------- /bin/utils/setup_study_folder.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/utils/setup_study_folder.sh -------------------------------------------------------------------------------- /bin/utils/validate_study_yaml.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/bin/utils/validate_study_yaml.py -------------------------------------------------------------------------------- /cluster.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/cluster.yaml -------------------------------------------------------------------------------- /data/combined_mutational_scans.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/combined_mutational_scans.tsv -------------------------------------------------------------------------------- /data/long_combined_mutational_scans.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/long_combined_mutational_scans.tsv -------------------------------------------------------------------------------- /data/pdb/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/README.md -------------------------------------------------------------------------------- /data/pdb/adrb2.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/adrb2.pdb -------------------------------------------------------------------------------- /data/pdb/amie.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/amie.pdb -------------------------------------------------------------------------------- /data/pdb/aph3ii.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/aph3ii.pdb -------------------------------------------------------------------------------- /data/pdb/braf.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/braf.pdb -------------------------------------------------------------------------------- /data/pdb/brca1.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/brca1.pdb -------------------------------------------------------------------------------- /data/pdb/calm1.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/calm1.pdb -------------------------------------------------------------------------------- /data/pdb/cbs.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/cbs.pdb -------------------------------------------------------------------------------- /data/pdb/ccr5.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/ccr5.pdb -------------------------------------------------------------------------------- /data/pdb/cp.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/cp.pdb -------------------------------------------------------------------------------- /data/pdb/cxcr4.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/cxcr4.pdb -------------------------------------------------------------------------------- /data/pdb/dbr1.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/dbr1.pdb -------------------------------------------------------------------------------- /data/pdb/gal4.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/gal4.pdb -------------------------------------------------------------------------------- /data/pdb/gfp.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/gfp.pdb -------------------------------------------------------------------------------- /data/pdb/ha.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/ha.pdb -------------------------------------------------------------------------------- /data/pdb/hsp90.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/hsp90.pdb -------------------------------------------------------------------------------- /data/pdb/infa.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/infa.pdb -------------------------------------------------------------------------------- /data/pdb/mapk1.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/mapk1.pdb -------------------------------------------------------------------------------- /data/pdb/np.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/np.pdb -------------------------------------------------------------------------------- /data/pdb/pab1.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/pab1.pdb -------------------------------------------------------------------------------- /data/pdb/proteing.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/proteing.pdb -------------------------------------------------------------------------------- /data/pdb/pten.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/pten.pdb -------------------------------------------------------------------------------- /data/pdb/ras.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/ras.pdb -------------------------------------------------------------------------------- /data/pdb/src.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/src.pdb -------------------------------------------------------------------------------- /data/pdb/ste12.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/ste12.pdb -------------------------------------------------------------------------------- /data/pdb/sumo1.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/sumo1.pdb -------------------------------------------------------------------------------- /data/pdb/tdp43.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/tdp43.pdb -------------------------------------------------------------------------------- /data/pdb/tem1.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/tem1.pdb -------------------------------------------------------------------------------- /data/pdb/tp53.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/tp53.pdb -------------------------------------------------------------------------------- /data/pdb/tpk1.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/tpk1.pdb -------------------------------------------------------------------------------- /data/pdb/tpmt.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/tpmt.pdb -------------------------------------------------------------------------------- /data/pdb/ube2i.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/ube2i.pdb -------------------------------------------------------------------------------- /data/pdb/ube4b.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/ube4b.pdb -------------------------------------------------------------------------------- /data/pdb/ubi.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/ubi.pdb -------------------------------------------------------------------------------- /data/pdb/yap1.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/pdb/yap1.pdb -------------------------------------------------------------------------------- /data/studies/ahler_2019_src/ahler_2019_src.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/ahler_2019_src/ahler_2019_src.yaml -------------------------------------------------------------------------------- /data/studies/ahler_2019_src/standardise_ahler_2019_src.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/ahler_2019_src/standardise_ahler_2019_src.R -------------------------------------------------------------------------------- /data/studies/araya_2012_yap1/araya_2012_yap1.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/araya_2012_yap1/araya_2012_yap1.yaml -------------------------------------------------------------------------------- /data/studies/araya_2012_yap1/standardise_araya_2012_yap1.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/araya_2012_yap1/standardise_araya_2012_yap1.R -------------------------------------------------------------------------------- /data/studies/ashenberg_2017_np/ashenberg_2017_np.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/ashenberg_2017_np/ashenberg_2017_np.yaml -------------------------------------------------------------------------------- /data/studies/ashenberg_2017_np/standardise_ashenberg_2017_np.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/ashenberg_2017_np/standardise_ashenberg_2017_np.R -------------------------------------------------------------------------------- /data/studies/bandaru_2017_ras/bandaru_2017_ras.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/bandaru_2017_ras/bandaru_2017_ras.yaml -------------------------------------------------------------------------------- /data/studies/bandaru_2017_ras/standardise_bandaru_2017_ras.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/bandaru_2017_ras/standardise_bandaru_2017_ras.R -------------------------------------------------------------------------------- /data/studies/bolognesi_2019_tdp43/bolognesi_2019_tdp43.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/bolognesi_2019_tdp43/bolognesi_2019_tdp43.yaml -------------------------------------------------------------------------------- /data/studies/bolognesi_2019_tdp43/standardise_bolognesi_2019_tdp43.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/bolognesi_2019_tdp43/standardise_bolognesi_2019_tdp43.R -------------------------------------------------------------------------------- /data/studies/brenan_2016_mapk1/brenan_2016_mapk1.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/brenan_2016_mapk1/brenan_2016_mapk1.yaml -------------------------------------------------------------------------------- /data/studies/brenan_2016_mapk1/standardise_brenan_2016_mapk1.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/brenan_2016_mapk1/standardise_brenan_2016_mapk1.R -------------------------------------------------------------------------------- /data/studies/dorrity_2018_ste12/dorrity_2018_ste12.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/dorrity_2018_ste12/dorrity_2018_ste12.yaml -------------------------------------------------------------------------------- /data/studies/dorrity_2018_ste12/standardise_dorrity_2018_ste12.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/dorrity_2018_ste12/standardise_dorrity_2018_ste12.R -------------------------------------------------------------------------------- /data/studies/doud_2015_np/doud_2015_np.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/doud_2015_np/doud_2015_np.yaml -------------------------------------------------------------------------------- /data/studies/doud_2015_np/standardise_doud_2015_np.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/doud_2015_np/standardise_doud_2015_np.R -------------------------------------------------------------------------------- /data/studies/findlay_2014_dbr1/findlay_2014_dbr1.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/findlay_2014_dbr1/findlay_2014_dbr1.yaml -------------------------------------------------------------------------------- /data/studies/findlay_2014_dbr1/standardise_findlay_2014_dbr1.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/findlay_2014_dbr1/standardise_findlay_2014_dbr1.R -------------------------------------------------------------------------------- /data/studies/findlay_2018_brca1/findlay_2018_brca1.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/findlay_2018_brca1/findlay_2018_brca1.yaml -------------------------------------------------------------------------------- /data/studies/findlay_2018_brca1/standardise_findlay_2018_brca1.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/findlay_2018_brca1/standardise_findlay_2018_brca1.R -------------------------------------------------------------------------------- /data/studies/firnberg_2014_tem1/firnberg_2014_tem1.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/firnberg_2014_tem1/firnberg_2014_tem1.yaml -------------------------------------------------------------------------------- /data/studies/firnberg_2014_tem1/standardise_firnberg_2014_tem1.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/firnberg_2014_tem1/standardise_firnberg_2014_tem1.R -------------------------------------------------------------------------------- /data/studies/giacomelli_2018_tp53/giacomelli_2018_tp53.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/giacomelli_2018_tp53/giacomelli_2018_tp53.yaml -------------------------------------------------------------------------------- /data/studies/giacomelli_2018_tp53/standardise_giacomelli_2018_tp53.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/giacomelli_2018_tp53/standardise_giacomelli_2018_tp53.R -------------------------------------------------------------------------------- /data/studies/hartman_2018_cp/hartman_2018_cp.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/hartman_2018_cp/hartman_2018_cp.yaml -------------------------------------------------------------------------------- /data/studies/hartman_2018_cp/standardise_hartman_2018_cp.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/hartman_2018_cp/standardise_hartman_2018_cp.R -------------------------------------------------------------------------------- /data/studies/heredia_2018_ccr5/heredia_2018_ccr5.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/heredia_2018_ccr5/heredia_2018_ccr5.yaml -------------------------------------------------------------------------------- /data/studies/heredia_2018_ccr5/standardise_heredia_2018_ccr5.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/heredia_2018_ccr5/standardise_heredia_2018_ccr5.R -------------------------------------------------------------------------------- /data/studies/heredia_2018_cxcr4/heredia_2018_cxcr4.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/heredia_2018_cxcr4/heredia_2018_cxcr4.yaml -------------------------------------------------------------------------------- /data/studies/heredia_2018_cxcr4/standardise_heredia_2018_cxcr4.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/heredia_2018_cxcr4/standardise_heredia_2018_cxcr4.R -------------------------------------------------------------------------------- /data/studies/hietpas_2011_hsp90/hietpas_2011_hsp90.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/hietpas_2011_hsp90/hietpas_2011_hsp90.yaml -------------------------------------------------------------------------------- /data/studies/hietpas_2011_hsp90/standardise_hietpas_2011_hsp90.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/hietpas_2011_hsp90/standardise_hietpas_2011_hsp90.R -------------------------------------------------------------------------------- /data/studies/jiang_2013_hsp90/jiang_2013_hsp90.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/jiang_2013_hsp90/jiang_2013_hsp90.yaml -------------------------------------------------------------------------------- /data/studies/jiang_2013_hsp90/standardise_jiang_2013_hsp90.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/jiang_2013_hsp90/standardise_jiang_2013_hsp90.R -------------------------------------------------------------------------------- /data/studies/jones_2019_adrb2/jones_2019_adrb2.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/jones_2019_adrb2/jones_2019_adrb2.yaml -------------------------------------------------------------------------------- /data/studies/jones_2019_adrb2/standardise_jones_2019_adrb2.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/jones_2019_adrb2/standardise_jones_2019_adrb2.R -------------------------------------------------------------------------------- /data/studies/kelsic_2016_infa/kelsic_2016_infa.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/kelsic_2016_infa/kelsic_2016_infa.yaml -------------------------------------------------------------------------------- /data/studies/kelsic_2016_infa/standardise_kelsic_2016_infa.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/kelsic_2016_infa/standardise_kelsic_2016_infa.R -------------------------------------------------------------------------------- /data/studies/kitzman_2015_gal4/kitzman_2015_gal4.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/kitzman_2015_gal4/kitzman_2015_gal4.yaml -------------------------------------------------------------------------------- /data/studies/kitzman_2015_gal4/standardise_kitzman_2015_gal4.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/kitzman_2015_gal4/standardise_kitzman_2015_gal4.R -------------------------------------------------------------------------------- /data/studies/lee_2018_ha/lee_2018_ha.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/lee_2018_ha/lee_2018_ha.yaml -------------------------------------------------------------------------------- /data/studies/lee_2018_ha/standardise_lee_2018_ha.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/lee_2018_ha/standardise_lee_2018_ha.R -------------------------------------------------------------------------------- /data/studies/matreyek_2018_pten/matreyek_2018_pten.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/matreyek_2018_pten/matreyek_2018_pten.yaml -------------------------------------------------------------------------------- /data/studies/matreyek_2018_pten/standardise_matreyek_2018_pten.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/matreyek_2018_pten/standardise_matreyek_2018_pten.R -------------------------------------------------------------------------------- /data/studies/matreyek_2018_tpmt/matreyek_2018_tpmt.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/matreyek_2018_tpmt/matreyek_2018_tpmt.yaml -------------------------------------------------------------------------------- /data/studies/matreyek_2018_tpmt/standardise_matreyek_2018_tpmt.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/matreyek_2018_tpmt/standardise_matreyek_2018_tpmt.R -------------------------------------------------------------------------------- /data/studies/melamed_2013_pab1/melamed_2013_pab1.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/melamed_2013_pab1/melamed_2013_pab1.yaml -------------------------------------------------------------------------------- /data/studies/melamed_2013_pab1/standardise_melamed_2013_pab1.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/melamed_2013_pab1/standardise_melamed_2013_pab1.R -------------------------------------------------------------------------------- /data/studies/melnikov_2014_aph3ii/melnikov_2014_aph3ii.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/melnikov_2014_aph3ii/melnikov_2014_aph3ii.yaml -------------------------------------------------------------------------------- /data/studies/melnikov_2014_aph3ii/standardise_melnikov_2014_aph3ii.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/melnikov_2014_aph3ii/standardise_melnikov_2014_aph3ii.R -------------------------------------------------------------------------------- /data/studies/mishra_2016_hsp90/mishra_2016_hsp90.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/mishra_2016_hsp90/mishra_2016_hsp90.yaml -------------------------------------------------------------------------------- /data/studies/mishra_2016_hsp90/standardise_mishra_2016_hsp90.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/mishra_2016_hsp90/standardise_mishra_2016_hsp90.R -------------------------------------------------------------------------------- /data/studies/olson_2014_proteing/olson_2014_proteing.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/olson_2014_proteing/olson_2014_proteing.yaml -------------------------------------------------------------------------------- /data/studies/olson_2014_proteing/standardise_olson_2014_proteing.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/olson_2014_proteing/standardise_olson_2014_proteing.R -------------------------------------------------------------------------------- /data/studies/roscoe_2013_ubi/roscoe_2013_ubi.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/roscoe_2013_ubi/roscoe_2013_ubi.yaml -------------------------------------------------------------------------------- /data/studies/roscoe_2013_ubi/standardise_roscoe_2013_ubi.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/roscoe_2013_ubi/standardise_roscoe_2013_ubi.R -------------------------------------------------------------------------------- /data/studies/roscoe_2014_ubi/roscoe_2014_ubi.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/roscoe_2014_ubi/roscoe_2014_ubi.yaml -------------------------------------------------------------------------------- /data/studies/roscoe_2014_ubi/standardise_roscoe_2014_ubi.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/roscoe_2014_ubi/standardise_roscoe_2014_ubi.R -------------------------------------------------------------------------------- /data/studies/sarkisyan_2016_gfp/sarkisyan_2016_gfp.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/sarkisyan_2016_gfp/sarkisyan_2016_gfp.yaml -------------------------------------------------------------------------------- /data/studies/sarkisyan_2016_gfp/standardise_sarkisyan_2016_gfp.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/sarkisyan_2016_gfp/standardise_sarkisyan_2016_gfp.R -------------------------------------------------------------------------------- /data/studies/starita_2013_ube4b/standardise_starita_2013_ube4b.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/starita_2013_ube4b/standardise_starita_2013_ube4b.R -------------------------------------------------------------------------------- /data/studies/starita_2013_ube4b/starita_2013_ube4b.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/starita_2013_ube4b/starita_2013_ube4b.yaml -------------------------------------------------------------------------------- /data/studies/starita_2015_brca1/standardise_starita_2015_brca1.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/starita_2015_brca1/standardise_starita_2015_brca1.R -------------------------------------------------------------------------------- /data/studies/starita_2015_brca1/starita_2015_brca1.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/starita_2015_brca1/starita_2015_brca1.yaml -------------------------------------------------------------------------------- /data/studies/steinberg_2016_tem1/standardise_steinberg_2016_tem1.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/steinberg_2016_tem1/standardise_steinberg_2016_tem1.R -------------------------------------------------------------------------------- /data/studies/steinberg_2016_tem1/steinberg_2016_tem1.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/steinberg_2016_tem1/steinberg_2016_tem1.yaml -------------------------------------------------------------------------------- /data/studies/sun_2018_cbs/standardise_sun_2018_cbs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/sun_2018_cbs/standardise_sun_2018_cbs.R -------------------------------------------------------------------------------- /data/studies/sun_2018_cbs/sun_2018_cbs.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/sun_2018_cbs/sun_2018_cbs.yaml -------------------------------------------------------------------------------- /data/studies/wagenaar_2014_braf/standardise_wagenaar_2014_braf.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/wagenaar_2014_braf/standardise_wagenaar_2014_braf.R -------------------------------------------------------------------------------- /data/studies/wagenaar_2014_braf/wagenaar_2014_braf.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/wagenaar_2014_braf/wagenaar_2014_braf.yaml -------------------------------------------------------------------------------- /data/studies/weile_2017_calm1/standardise_weile_2017_calm1.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/weile_2017_calm1/standardise_weile_2017_calm1.R -------------------------------------------------------------------------------- /data/studies/weile_2017_calm1/weile_2017_calm1.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/weile_2017_calm1/weile_2017_calm1.yaml -------------------------------------------------------------------------------- /data/studies/weile_2017_sumo1/standardise_weile_2017_sumo1.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/weile_2017_sumo1/standardise_weile_2017_sumo1.R -------------------------------------------------------------------------------- /data/studies/weile_2017_sumo1/weile_2017_sumo1.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/weile_2017_sumo1/weile_2017_sumo1.yaml -------------------------------------------------------------------------------- /data/studies/weile_2017_tpk1/standardise_weile_2017_tpk1.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/weile_2017_tpk1/standardise_weile_2017_tpk1.R -------------------------------------------------------------------------------- /data/studies/weile_2017_tpk1/weile_2017_tpk1.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/weile_2017_tpk1/weile_2017_tpk1.yaml -------------------------------------------------------------------------------- /data/studies/weile_2017_ube2i/standardise_weile_2017_ube2i.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/weile_2017_ube2i/standardise_weile_2017_ube2i.R -------------------------------------------------------------------------------- /data/studies/weile_2017_ube2i/weile_2017_ube2i.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/weile_2017_ube2i/weile_2017_ube2i.yaml -------------------------------------------------------------------------------- /data/studies/wrenbeck_2017_amie/standardise_wrenbeck_2017_amie.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/wrenbeck_2017_amie/standardise_wrenbeck_2017_amie.R -------------------------------------------------------------------------------- /data/studies/wrenbeck_2017_amie/wrenbeck_2017_amie.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/studies/wrenbeck_2017_amie/wrenbeck_2017_amie.yaml -------------------------------------------------------------------------------- /data/subtypes/final_subtypes.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/subtypes/final_subtypes.tsv -------------------------------------------------------------------------------- /data/subtypes/sift_scores.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/data/subtypes/sift_scores.tsv -------------------------------------------------------------------------------- /docs/combined_mutational_scans_readme.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/docs/combined_mutational_scans_readme.txt -------------------------------------------------------------------------------- /docs/foldx_eqn.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/docs/foldx_eqn.md -------------------------------------------------------------------------------- /docs/subtype_descriptions.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/docs/subtype_descriptions.md -------------------------------------------------------------------------------- /docs/subtypes_readme.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/docs/subtypes_readme.txt -------------------------------------------------------------------------------- /figures/4_figures/parts/arrow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/parts/arrow.png -------------------------------------------------------------------------------- /figures/4_figures/position_examples/adrb2_ala_small_hydro.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/position_examples/adrb2_ala_small_hydro.png -------------------------------------------------------------------------------- /figures/4_figures/position_examples/adrb2_domains.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/position_examples/adrb2_domains.png -------------------------------------------------------------------------------- /figures/4_figures/position_examples/aph3ii_arg_not_proline.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/position_examples/aph3ii_arg_not_proline.png -------------------------------------------------------------------------------- /figures/4_figures/position_examples/cbs_asp_ionic.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/position_examples/cbs_asp_ionic.png -------------------------------------------------------------------------------- /figures/4_figures/position_examples/cbs_phe_pi.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/position_examples/cbs_phe_pi.png -------------------------------------------------------------------------------- /figures/4_figures/position_examples/ccr5_cys_aromatic.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/position_examples/ccr5_cys_aromatic.png -------------------------------------------------------------------------------- /figures/4_figures/position_examples/ccr5_cys_disulphide.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/position_examples/ccr5_cys_disulphide.png -------------------------------------------------------------------------------- /figures/4_figures/position_examples/ccr5_domains.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/position_examples/ccr5_domains.png -------------------------------------------------------------------------------- /figures/4_figures/position_examples/cxcr4_domains.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/position_examples/cxcr4_domains.png -------------------------------------------------------------------------------- /figures/4_figures/position_examples/gal4_cys_zinc.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/position_examples/gal4_cys_zinc.png -------------------------------------------------------------------------------- /figures/4_figures/position_examples/np_cys_aromatic.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/position_examples/np_cys_aromatic.png -------------------------------------------------------------------------------- /figures/4_figures/position_examples/pab1_arg_not_neg.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/position_examples/pab1_arg_not_neg.png -------------------------------------------------------------------------------- /figures/4_figures/position_examples/ras_aliphatic_entropy.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/position_examples/ras_aliphatic_entropy.png -------------------------------------------------------------------------------- /figures/4_figures/position_examples/ras_met_buried.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/position_examples/ras_met_buried.png -------------------------------------------------------------------------------- /figures/4_figures/position_examples/tem1_asp_ligand.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/position_examples/tem1_asp_ligand.png -------------------------------------------------------------------------------- /figures/4_figures/position_examples/tem1_asp_sa.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/position_examples/tem1_asp_sa.png -------------------------------------------------------------------------------- /figures/4_figures/proteins/adrb2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/proteins/adrb2.png -------------------------------------------------------------------------------- /figures/4_figures/proteins/amie.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/proteins/amie.png -------------------------------------------------------------------------------- /figures/4_figures/proteins/aph3ii.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/proteins/aph3ii.png -------------------------------------------------------------------------------- /figures/4_figures/proteins/brca1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/proteins/brca1.png -------------------------------------------------------------------------------- /figures/4_figures/proteins/calm1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/proteins/calm1.png -------------------------------------------------------------------------------- /figures/4_figures/proteins/cbs.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/proteins/cbs.png -------------------------------------------------------------------------------- /figures/4_figures/proteins/ccr5.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/proteins/ccr5.png -------------------------------------------------------------------------------- /figures/4_figures/proteins/cp.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/proteins/cp.png -------------------------------------------------------------------------------- /figures/4_figures/proteins/cxcr4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/proteins/cxcr4.png -------------------------------------------------------------------------------- /figures/4_figures/proteins/dbr1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/proteins/dbr1.png -------------------------------------------------------------------------------- /figures/4_figures/proteins/gal4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/proteins/gal4.png -------------------------------------------------------------------------------- /figures/4_figures/proteins/ha.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/proteins/ha.png -------------------------------------------------------------------------------- /figures/4_figures/proteins/hsp90.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/proteins/hsp90.png -------------------------------------------------------------------------------- /figures/4_figures/proteins/infa.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/proteins/infa.png -------------------------------------------------------------------------------- /figures/4_figures/proteins/np.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/proteins/np.png -------------------------------------------------------------------------------- /figures/4_figures/proteins/pab1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/proteins/pab1.png -------------------------------------------------------------------------------- /figures/4_figures/proteins/proteing.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/proteins/proteing.png -------------------------------------------------------------------------------- /figures/4_figures/proteins/pten.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/proteins/pten.png -------------------------------------------------------------------------------- /figures/4_figures/proteins/ras.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/proteins/ras.png -------------------------------------------------------------------------------- /figures/4_figures/proteins/src.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/proteins/src.png -------------------------------------------------------------------------------- /figures/4_figures/proteins/ste12.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/proteins/ste12.png -------------------------------------------------------------------------------- /figures/4_figures/proteins/sumo1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/proteins/sumo1.png -------------------------------------------------------------------------------- /figures/4_figures/proteins/tem1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/proteins/tem1.png -------------------------------------------------------------------------------- /figures/4_figures/proteins/tp53.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/proteins/tp53.png -------------------------------------------------------------------------------- /figures/4_figures/proteins/tpk1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/proteins/tpk1.png -------------------------------------------------------------------------------- /figures/4_figures/proteins/tpmt.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/proteins/tpmt.png -------------------------------------------------------------------------------- /figures/4_figures/proteins/ube2i.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/proteins/ube2i.png -------------------------------------------------------------------------------- /figures/4_figures/proteins/ube4b.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/proteins/ube4b.png -------------------------------------------------------------------------------- /figures/4_figures/proteins/ubi.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/proteins/ubi.png -------------------------------------------------------------------------------- /figures/4_figures/proteins/yap1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/4_figures/proteins/yap1.png -------------------------------------------------------------------------------- /figures/5_thesis/figure1_1.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/5_thesis/figure1_1.svg -------------------------------------------------------------------------------- /figures/summary.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/figures/summary.svg -------------------------------------------------------------------------------- /meta/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/README.md -------------------------------------------------------------------------------- /meta/fasta/H3N2_A_Aichi_2_1968_np.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/H3N2_A_Aichi_2_1968_np.fa -------------------------------------------------------------------------------- /meta/fasta/H3N2_A_Perth_16_2009_ha.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/H3N2_A_Perth_16_2009_ha.fa -------------------------------------------------------------------------------- /meta/fasta/a_victoria_gfp.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/a_victoria_gfp.fa -------------------------------------------------------------------------------- /meta/fasta/b_subtilis_gdh.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/b_subtilis_gdh.fa -------------------------------------------------------------------------------- /meta/fasta/bacteriophage_ms2_cp.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/bacteriophage_ms2_cp.fa -------------------------------------------------------------------------------- /meta/fasta/e_coli_aph3ii.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/e_coli_aph3ii.fa -------------------------------------------------------------------------------- /meta/fasta/e_coli_ccdb.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/e_coli_ccdb.fa -------------------------------------------------------------------------------- /meta/fasta/e_coli_infa.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/e_coli_infa.fa -------------------------------------------------------------------------------- /meta/fasta/e_coli_tem1.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/e_coli_tem1.fa -------------------------------------------------------------------------------- /meta/fasta/h_sapiens_adrb2.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/h_sapiens_adrb2.fa -------------------------------------------------------------------------------- /meta/fasta/h_sapiens_braf.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/h_sapiens_braf.fa -------------------------------------------------------------------------------- /meta/fasta/h_sapiens_brca1.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/h_sapiens_brca1.fa -------------------------------------------------------------------------------- /meta/fasta/h_sapiens_calm1.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/h_sapiens_calm1.fa -------------------------------------------------------------------------------- /meta/fasta/h_sapiens_cbs.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/h_sapiens_cbs.fa -------------------------------------------------------------------------------- /meta/fasta/h_sapiens_ccr5.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/h_sapiens_ccr5.fa -------------------------------------------------------------------------------- /meta/fasta/h_sapiens_cxcr4.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/h_sapiens_cxcr4.fa -------------------------------------------------------------------------------- /meta/fasta/h_sapiens_dbr1.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/h_sapiens_dbr1.fa -------------------------------------------------------------------------------- /meta/fasta/h_sapiens_mapk1.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/h_sapiens_mapk1.fa -------------------------------------------------------------------------------- /meta/fasta/h_sapiens_pten.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/h_sapiens_pten.fa -------------------------------------------------------------------------------- /meta/fasta/h_sapiens_ras.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/h_sapiens_ras.fa -------------------------------------------------------------------------------- /meta/fasta/h_sapiens_src.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/h_sapiens_src.fa -------------------------------------------------------------------------------- /meta/fasta/h_sapiens_sumo1.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/h_sapiens_sumo1.fa -------------------------------------------------------------------------------- /meta/fasta/h_sapiens_tdp43.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/h_sapiens_tdp43.fa -------------------------------------------------------------------------------- /meta/fasta/h_sapiens_tp53.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/h_sapiens_tp53.fa -------------------------------------------------------------------------------- /meta/fasta/h_sapiens_tpk1.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/h_sapiens_tpk1.fa -------------------------------------------------------------------------------- /meta/fasta/h_sapiens_tpmt.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/h_sapiens_tpmt.fa -------------------------------------------------------------------------------- /meta/fasta/h_sapiens_ube2i.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/h_sapiens_ube2i.fa -------------------------------------------------------------------------------- /meta/fasta/h_sapiens_yap1.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/h_sapiens_yap1.fa -------------------------------------------------------------------------------- /meta/fasta/m_musculus_ube4b.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/m_musculus_ube4b.fa -------------------------------------------------------------------------------- /meta/fasta/p_aeruginosa_amie.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/p_aeruginosa_amie.fa -------------------------------------------------------------------------------- /meta/fasta/s_cerevisiae_gal4.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/s_cerevisiae_gal4.fa -------------------------------------------------------------------------------- /meta/fasta/s_cerevisiae_gcn4.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/s_cerevisiae_gcn4.fa -------------------------------------------------------------------------------- /meta/fasta/s_cerevisiae_hsc82.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/s_cerevisiae_hsc82.fa -------------------------------------------------------------------------------- /meta/fasta/s_cerevisiae_hsp90.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/s_cerevisiae_hsp90.fa -------------------------------------------------------------------------------- /meta/fasta/s_cerevisiae_pab1.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/s_cerevisiae_pab1.fa -------------------------------------------------------------------------------- /meta/fasta/s_cerevisiae_ste12.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/s_cerevisiae_ste12.fa -------------------------------------------------------------------------------- /meta/fasta/s_cerevisiae_ubi.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/s_cerevisiae_ubi.fa -------------------------------------------------------------------------------- /meta/fasta/s_pyrogenes_cas9.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/s_pyrogenes_cas9.fa -------------------------------------------------------------------------------- /meta/fasta/strep_protein_g_precursor.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/strep_protein_g_precursor.fa -------------------------------------------------------------------------------- /meta/fasta/streptococcus_proteing.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/fasta/streptococcus_proteing.fa -------------------------------------------------------------------------------- /meta/final_subtypes.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/final_subtypes.yaml -------------------------------------------------------------------------------- /meta/residue_hydrophobicity.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/residue_hydrophobicity.tsv -------------------------------------------------------------------------------- /meta/structures.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/structures.yaml -------------------------------------------------------------------------------- /meta/study_template.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/study_template.yaml -------------------------------------------------------------------------------- /meta/subtypes/gmm_pca.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/subtypes/gmm_pca.yaml -------------------------------------------------------------------------------- /meta/subtypes/gmm_pca_no_sig.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/subtypes/gmm_pca_no_sig.yaml -------------------------------------------------------------------------------- /meta/subtypes/gmm_profile.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/subtypes/gmm_profile.yaml -------------------------------------------------------------------------------- /meta/subtypes/hclust_pca_dynamic.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/subtypes/hclust_pca_dynamic.yaml -------------------------------------------------------------------------------- /meta/subtypes/hclust_pca_no_sig_dynamic.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/subtypes/hclust_pca_no_sig_dynamic.yaml -------------------------------------------------------------------------------- /meta/subtypes/hclust_pca_no_sig_dynamic_cos_deep_0.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/subtypes/hclust_pca_no_sig_dynamic_cos_deep_0.yaml -------------------------------------------------------------------------------- /meta/subtypes/hclust_pca_no_sig_dynamic_cos_deep_1.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/subtypes/hclust_pca_no_sig_dynamic_cos_deep_1.yaml -------------------------------------------------------------------------------- /meta/subtypes/hclust_profile_dynamic.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/subtypes/hclust_profile_dynamic.yaml -------------------------------------------------------------------------------- /meta/subtypes/hclust_profile_dynamic_cos.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/subtypes/hclust_profile_dynamic_cos.yaml -------------------------------------------------------------------------------- /meta/subtypes/hdbscan_pca.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/subtypes/hdbscan_pca.yaml -------------------------------------------------------------------------------- /meta/subtypes/hdbscan_pca_no_sig.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/subtypes/hdbscan_pca_no_sig.yaml -------------------------------------------------------------------------------- /meta/subtypes/hdbscan_profile.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/subtypes/hdbscan_profile.yaml -------------------------------------------------------------------------------- /meta/subtypes/kmeans_pca.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/subtypes/kmeans_pca.yaml -------------------------------------------------------------------------------- /meta/subtypes/kmeans_pca_no_sig.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/subtypes/kmeans_pca_no_sig.yaml -------------------------------------------------------------------------------- /meta/subtypes/kmeans_profile.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/subtypes/kmeans_profile.yaml -------------------------------------------------------------------------------- /meta/subtypes/pam_pca_no_sig_cos.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/subtypes/pam_pca_no_sig_cos.yaml -------------------------------------------------------------------------------- /meta/subtypes/pam_pca_no_sig_man.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/subtypes/pam_pca_no_sig_man.yaml -------------------------------------------------------------------------------- /meta/subtypes/pam_profile_cos.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/subtypes/pam_profile_cos.yaml -------------------------------------------------------------------------------- /meta/subtypes/pam_profile_man.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/subtypes/pam_profile_man.yaml -------------------------------------------------------------------------------- /meta/uniprot_domains.gff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/uniprot_domains.gff -------------------------------------------------------------------------------- /meta/uniprot_ptms.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/meta/uniprot_ptms.tsv -------------------------------------------------------------------------------- /snakemake.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/snakemake.yaml -------------------------------------------------------------------------------- /src/chemical_environment.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/src/chemical_environment.py -------------------------------------------------------------------------------- /src/colour_spectrum.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/src/colour_spectrum.py -------------------------------------------------------------------------------- /src/config.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/src/config.R -------------------------------------------------------------------------------- /src/continuous.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/src/continuous.R -------------------------------------------------------------------------------- /src/dimensionality_reduction.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/src/dimensionality_reduction.R -------------------------------------------------------------------------------- /src/pymol_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/src/pymol_utils.py -------------------------------------------------------------------------------- /src/study_standardising.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/src/study_standardising.R -------------------------------------------------------------------------------- /src/subtype_characterisation.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/src/subtype_characterisation.R -------------------------------------------------------------------------------- /src/subtype_clustering.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/src/subtype_clustering.R -------------------------------------------------------------------------------- /src/subtypes_utils.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/src/subtypes_utils.R -------------------------------------------------------------------------------- /src/subtypes_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allydunham/aa_subtypes/HEAD/src/subtypes_utils.py --------------------------------------------------------------------------------