├── .github └── workflows │ ├── python-app-py311.yml │ └── python-pytest-report.yml ├── .gitignore ├── .readthedocs.yml ├── Adaptive2020.tsv ├── Dockerfile ├── LICENSE ├── README.md ├── dash.csv ├── dash2.csv ├── dash_beta_airr.csv ├── dash_human.csv ├── docs ├── E3.jpg ├── Makefile ├── NP_gene_usage_plot.svg ├── PA_gene_usage_plot.svg ├── _static │ ├── PA1.png │ ├── PA2.png │ ├── hierdiff_example.html │ ├── hierdiff_example_PA_v_PB1.html │ ├── mira_epitope_48_610_YLQPRTFL_YLQPRTFLL_YYVGYLQPRTF.tcrdist3.csv.ecdf_AER_plot.png │ ├── mira_epitope_48_610_YLQPRTFL_YLQPRTFLL_YYVGYLQPRTF.tcrdist3.csv.ecdf_BUR_plot.png │ ├── mira_epitope_48_610_YLQPRTFL_YLQPRTFLL_YYVGYLQPRTF.tcrdist3.csv.ranked_centers_bkgd_ctlr_1E6.html │ ├── nlog10_pgen_vs_neighbors_pw_ab_50.png │ ├── nlog10_pgen_vs_neighbors_pw_b_18.png │ ├── quasi_public_clones.html │ ├── quasi_public_clones2.html │ ├── quasi_public_clones3.html │ ├── quasi_public_clones_PA.html │ ├── test.svg │ └── testraw.svg ├── adaptive.rst ├── breadth.rst ├── bulkdata.rst ├── conf.py ├── diversity.rst ├── docker.rst ├── downloads.rst ├── index.rst ├── influenza_example.rst ├── inputs.rst ├── join.rst ├── make.bat ├── metaclonotype-tabulation.py ├── metaclonotypes.py ├── metaclonotypes.rst ├── motif_gallery.rst ├── nn_PA_example_tcrdist150.png ├── nn_PA_example_tcrdist75.png ├── pGen.rst ├── plotpairing1.svg ├── plotpairing2.svg ├── plotpairing4.svg ├── public.rst ├── radius.rst ├── real_bulk_example.py ├── requirements.txt ├── simulate.rst ├── sparse.py ├── sparsity.rst ├── tcrdistances.rst ├── tree.rst ├── vdjtools.rst ├── visualizing.rst ├── welcome.rst └── workflow.rst ├── requirements.txt ├── rhesus.csv ├── sant.csv ├── setup.py └── tcrdist ├── __init__.py ├── adpt_funcs.py ├── automate.py ├── background.py ├── breadth.py ├── centers.py ├── data ├── __init__.py ├── covid19 │ ├── __init__.py │ ├── m60_bkgd_test_input.csv │ ├── m60_test_input.csv │ ├── mira_epitope_10_2274_LSPRWYFYY_SPRWYFYYL.tcrdist3.csv │ ├── mira_epitope_110_148_ELIRQGTDY_QELIRQGTDY_QELIRQGTDYKHW.tcrdist3.csv │ ├── mira_epitope_111_146_AEIPKEEVKPF_ASKIITLKK_SASKIITLK.tcrdist3.csv │ ├── mira_epitope_118_136_ALNTPKDHI_ATEGALNTPK.tcrdist3.csv │ ├── mira_epitope_133_102_NQKLIANQF.tcrdist3.csv │ ├── mira_epitope_140_92_NSSPDDQIGY_NTNSSPDDQIGYY_SSPDDQIGY_SSPDDQIGYY.tcrdist3.csv │ ├── mira_epitope_147_73_DLFMRIFTI_MDLFMRIFTI.tcrdist3.csv │ ├── mira_epitope_155_59_RARSVSPKL_SVSPKLFIR.tcrdist3.csv │ ├── mira_epitope_16_1683_QYIKWPWYI_YEQYIKWPW_YEQYIKWPWY.tcrdist3.csv │ ├── mira_epitope_176_44_SSTFNVPMEKLK.tcrdist3.csv │ ├── mira_epitope_183_39_RIRGGDGKM_RIRGGDGKMK.tcrdist3.csv │ ├── mira_epitope_185_39_ASQRVAGDSGFAAY_DSGFAAYSR_VAGDSGFAAY.tcrdist3.csv │ ├── mira_epitope_18_1578_FPNITNLCPF_QPTESIVRF_RFPNITNLCPF_TESIVRFPNI_VQPTESIVRF_VRFPNITNL.tcrdist3.csv │ ├── mira_epitope_192_31_FQPTNGVGY.tcrdist3.csv │ ├── mira_epitope_1_8260_HTTDPSFLGRY.tcrdist3.csv │ ├── mira_epitope_29_1097_TVLSFCAFA_VLSFCAFAV.tcrdist3.csv │ ├── mira_epitope_30_1064_KAYNVTQAF.tcrdist3.csv │ ├── mira_epitope_37_818_FGEVFNATRF_FNATRFASVY_GEVFNATRF_NATRFASVY.tcrdist3.csv │ ├── mira_epitope_44_697_FPPTSFGPL.tcrdist3.csv │ ├── mira_epitope_45_689_SYFTSDYYQL_VLHSYFTSDY_YFTSDYYQLY.tcrdist3.csv │ ├── mira_epitope_48_610_YLQPRTFL_YLQPRTFLL_YYVGYLQPRTF.tcrdist3.csv │ ├── mira_epitope_51_546_AYKTFPPTEPK_KTFPPTEPK.tcrdist3.csv │ ├── mira_epitope_53_532_NYLYRLFRK_NYNYLYRLF.tcrdist3.csv │ ├── mira_epitope_55_524_ALRKVPTDNYITTY_KVPTDNYITTY.tcrdist3.csv │ ├── mira_epitope_55_524_ALRKVPTDNYITTY_KVPTDNYITTY.tcrdist3.csv.bE5ctrl.centers.csv │ ├── mira_epitope_55_524_ALRKVPTDNYITTY_KVPTDNYITTY.tcrdist3.csv.bE5ctrl.centers.csv.ranked_centers.tsv │ ├── mira_epitope_55_524_ALRKVPTDNYITTY_KVPTDNYITTY.tcrdist3.radius.csv │ ├── mira_epitope_67_382_APHGVVFL_APHGVVFLHV_GVVFLHVTY_VVFLHVTYV.tcrdist3.csv │ ├── mira_epitope_70_345_DTDFVNEFYAY_NRDVDTDFVNEFY.tcrdist3.csv │ ├── mira_epitope_90_216_GYQPYRVVVL_PYRVVVLSF_QPYRVVVL_QPYRVVVLSF.tcrdist3.csv │ ├── mira_epitope_99_191_QECVRGTTVL.tcrdist3.csv │ └── mira_epitope_9_2477_FLQSINFVR_FLQSINFVRI_FLYLYALVYF_GLEAPFLYLY_INFVRIIMR_LQSINFVRI_LQSINFVRII_QSINFVRII_SINFVRIIMR_VYFLQSINF_VYFLQSINFV_YFLQSINFVR_YLYALVYFL.tcrdist3.csv └── formats │ ├── vdj.M_15_CD8_alpha.clonotypes.TRA.txt.gz │ └── vdj.M_15_CD8_beta.clonotypes.TRB.txt.gz ├── db ├── __init__.py ├── adaptive_imgt_mapping.csv ├── alphabeta_gammadelta_db.tsv ├── combo_db.tsv ├── combo_xcr_2023-12-30.tsv └── combo_xcr_2024-03-05.tsv ├── default_models ├── __init__.py ├── human_B_heavy │ ├── J_gene_CDR3_anchors.csv │ ├── V_gene_CDR3_anchors.csv │ ├── __init__.py │ ├── model_marginals.txt │ └── model_params.txt ├── human_T_alpha │ ├── J_gene_CDR3_anchors.csv │ ├── V_gene_CDR3_anchors.csv │ ├── __init__.py │ ├── model_marginals.txt │ └── model_params.txt ├── human_T_beta │ ├── J_gene_CDR3_anchors.csv │ ├── V_gene_CDR3_anchors.csv │ ├── __init__.py │ ├── model_marginals.txt │ └── model_params.txt ├── mouse_T_alpha │ ├── J_gene_CDR3_anchors.csv │ ├── V_gene_CDR3_anchors.csv │ ├── __init__.py │ ├── model_marginals.txt │ └── model_params.txt └── mouse_T_beta │ ├── J_gene_CDR3_anchors.csv │ ├── V_gene_CDR3_anchors.csv │ ├── __init__.py │ ├── model_marginals.txt │ └── model_params.txt ├── diversity.py ├── ecdf.py ├── gene_pairing_plot.py ├── html_colors.py ├── join.py ├── mappers.py ├── memory.py ├── neighbors.py ├── olga_directed.py ├── olga_load_model.py ├── paths.py ├── pgen.py ├── plotting.py ├── public.py ├── regex.py ├── rep_diff.py ├── rep_funcs.py ├── repertoire.py ├── repertoire_db.py ├── sample.py ├── setup_tests.py ├── sparse.py ├── speed.py ├── summarize.py ├── swap_gene_name.py ├── tabulate.py ├── tests ├── __init__.py ├── longtest_pgen_parallel.py ├── longtest_simulate_cdr3_w_olga.py ├── test_automatic.py ├── test_background.py ├── test_breadth.py ├── test_bulkdata.py ├── test_centers.py ├── test_diversity.py ├── test_downloads.py ├── test_ecdf_example.py ├── test_example_1.py ├── test_example_10.py ├── test_example_11.py ├── test_example_12.py ├── test_example_13.py ├── test_example_14.py ├── test_example_15.py ├── test_example_16.py ├── test_example_17.py ├── test_example_18.py ├── test_example_19.py ├── test_example_2.py ├── test_example_20.py ├── test_example_21.py ├── test_example_22.py ├── test_example_23.py ├── test_example_24_centers.py ├── test_example_3.py ├── test_example_4.py ├── test_example_5.py ├── test_example_6.py ├── test_example_7.py ├── test_example_8.py ├── test_example_9.py ├── test_gallery_hdiff.py ├── test_introduction_1.py ├── test_introduction_2.py ├── test_introduction_3.py ├── test_introduction_4.py ├── test_introduction_5.py ├── test_introduction_6.py ├── test_join.py ├── test_memory.py ├── test_neighbors.py ├── test_olga_synthetic.py ├── test_out_of_memory_features.py ├── test_pgen_1.py ├── test_pgen_mouse.py ├── test_public.py ├── test_regex.py ├── test_rep_funcs.py ├── test_repertoire.py ├── test_repertoire_db.py ├── test_rhesus.py ├── test_setup_tests.py ├── test_sparse_pwrect.py ├── test_summarize.py ├── test_translation.py ├── test_tree.py ├── test_vdj_funcs.py ├── test_workflow_1.py └── test_workflow_2.py ├── translation.py ├── tree.py └── vdjtools_funcs.py /.github/workflows/python-app-py311.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/.github/workflows/python-app-py311.yml -------------------------------------------------------------------------------- /.github/workflows/python-pytest-report.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/.github/workflows/python-pytest-report.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/.gitignore -------------------------------------------------------------------------------- /.readthedocs.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/.readthedocs.yml -------------------------------------------------------------------------------- /Adaptive2020.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/Adaptive2020.tsv -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/Dockerfile -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/README.md -------------------------------------------------------------------------------- /dash.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/dash.csv -------------------------------------------------------------------------------- /dash2.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/dash2.csv -------------------------------------------------------------------------------- /dash_beta_airr.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/dash_beta_airr.csv -------------------------------------------------------------------------------- /dash_human.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/dash_human.csv -------------------------------------------------------------------------------- /docs/E3.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/E3.jpg -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/Makefile -------------------------------------------------------------------------------- /docs/NP_gene_usage_plot.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/NP_gene_usage_plot.svg -------------------------------------------------------------------------------- /docs/PA_gene_usage_plot.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/PA_gene_usage_plot.svg -------------------------------------------------------------------------------- /docs/_static/PA1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/_static/PA1.png -------------------------------------------------------------------------------- /docs/_static/PA2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/_static/PA2.png -------------------------------------------------------------------------------- /docs/_static/hierdiff_example.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/_static/hierdiff_example.html -------------------------------------------------------------------------------- /docs/_static/hierdiff_example_PA_v_PB1.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/_static/hierdiff_example_PA_v_PB1.html -------------------------------------------------------------------------------- /docs/_static/mira_epitope_48_610_YLQPRTFL_YLQPRTFLL_YYVGYLQPRTF.tcrdist3.csv.ecdf_AER_plot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/_static/mira_epitope_48_610_YLQPRTFL_YLQPRTFLL_YYVGYLQPRTF.tcrdist3.csv.ecdf_AER_plot.png -------------------------------------------------------------------------------- /docs/_static/mira_epitope_48_610_YLQPRTFL_YLQPRTFLL_YYVGYLQPRTF.tcrdist3.csv.ecdf_BUR_plot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/_static/mira_epitope_48_610_YLQPRTFL_YLQPRTFLL_YYVGYLQPRTF.tcrdist3.csv.ecdf_BUR_plot.png -------------------------------------------------------------------------------- /docs/_static/mira_epitope_48_610_YLQPRTFL_YLQPRTFLL_YYVGYLQPRTF.tcrdist3.csv.ranked_centers_bkgd_ctlr_1E6.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/_static/mira_epitope_48_610_YLQPRTFL_YLQPRTFLL_YYVGYLQPRTF.tcrdist3.csv.ranked_centers_bkgd_ctlr_1E6.html -------------------------------------------------------------------------------- /docs/_static/nlog10_pgen_vs_neighbors_pw_ab_50.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/_static/nlog10_pgen_vs_neighbors_pw_ab_50.png -------------------------------------------------------------------------------- /docs/_static/nlog10_pgen_vs_neighbors_pw_b_18.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/_static/nlog10_pgen_vs_neighbors_pw_b_18.png -------------------------------------------------------------------------------- /docs/_static/quasi_public_clones.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/_static/quasi_public_clones.html -------------------------------------------------------------------------------- /docs/_static/quasi_public_clones2.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/_static/quasi_public_clones2.html -------------------------------------------------------------------------------- /docs/_static/quasi_public_clones3.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/_static/quasi_public_clones3.html -------------------------------------------------------------------------------- /docs/_static/quasi_public_clones_PA.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/_static/quasi_public_clones_PA.html -------------------------------------------------------------------------------- /docs/_static/test.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/_static/test.svg -------------------------------------------------------------------------------- /docs/_static/testraw.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/_static/testraw.svg -------------------------------------------------------------------------------- /docs/adaptive.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/adaptive.rst -------------------------------------------------------------------------------- /docs/breadth.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/breadth.rst -------------------------------------------------------------------------------- /docs/bulkdata.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/bulkdata.rst -------------------------------------------------------------------------------- /docs/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/conf.py -------------------------------------------------------------------------------- /docs/diversity.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/diversity.rst -------------------------------------------------------------------------------- /docs/docker.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/docker.rst -------------------------------------------------------------------------------- /docs/downloads.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/downloads.rst -------------------------------------------------------------------------------- /docs/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/index.rst -------------------------------------------------------------------------------- /docs/influenza_example.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/influenza_example.rst -------------------------------------------------------------------------------- /docs/inputs.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/inputs.rst -------------------------------------------------------------------------------- /docs/join.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/join.rst -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/make.bat -------------------------------------------------------------------------------- /docs/metaclonotype-tabulation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/metaclonotype-tabulation.py -------------------------------------------------------------------------------- /docs/metaclonotypes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/metaclonotypes.py -------------------------------------------------------------------------------- /docs/metaclonotypes.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/metaclonotypes.rst -------------------------------------------------------------------------------- /docs/motif_gallery.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/motif_gallery.rst -------------------------------------------------------------------------------- /docs/nn_PA_example_tcrdist150.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/nn_PA_example_tcrdist150.png -------------------------------------------------------------------------------- /docs/nn_PA_example_tcrdist75.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/nn_PA_example_tcrdist75.png -------------------------------------------------------------------------------- /docs/pGen.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/pGen.rst -------------------------------------------------------------------------------- /docs/plotpairing1.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/plotpairing1.svg -------------------------------------------------------------------------------- /docs/plotpairing2.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/plotpairing2.svg -------------------------------------------------------------------------------- /docs/plotpairing4.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/plotpairing4.svg -------------------------------------------------------------------------------- /docs/public.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/public.rst -------------------------------------------------------------------------------- /docs/radius.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/radius.rst -------------------------------------------------------------------------------- /docs/real_bulk_example.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/real_bulk_example.py -------------------------------------------------------------------------------- /docs/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/requirements.txt -------------------------------------------------------------------------------- /docs/simulate.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/simulate.rst -------------------------------------------------------------------------------- /docs/sparse.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/sparse.py -------------------------------------------------------------------------------- /docs/sparsity.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/sparsity.rst -------------------------------------------------------------------------------- /docs/tcrdistances.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/tcrdistances.rst -------------------------------------------------------------------------------- /docs/tree.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/tree.rst -------------------------------------------------------------------------------- /docs/vdjtools.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/vdjtools.rst -------------------------------------------------------------------------------- /docs/visualizing.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/visualizing.rst -------------------------------------------------------------------------------- /docs/welcome.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/welcome.rst -------------------------------------------------------------------------------- /docs/workflow.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/docs/workflow.rst -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/requirements.txt -------------------------------------------------------------------------------- /rhesus.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/rhesus.csv -------------------------------------------------------------------------------- /sant.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/sant.csv -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/setup.py -------------------------------------------------------------------------------- /tcrdist/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tcrdist/adpt_funcs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/adpt_funcs.py -------------------------------------------------------------------------------- /tcrdist/automate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/automate.py -------------------------------------------------------------------------------- /tcrdist/background.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/background.py -------------------------------------------------------------------------------- /tcrdist/breadth.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/breadth.py -------------------------------------------------------------------------------- /tcrdist/centers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/centers.py -------------------------------------------------------------------------------- /tcrdist/data/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tcrdist/data/covid19/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tcrdist/data/covid19/m60_bkgd_test_input.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/m60_bkgd_test_input.csv -------------------------------------------------------------------------------- /tcrdist/data/covid19/m60_test_input.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/m60_test_input.csv -------------------------------------------------------------------------------- /tcrdist/data/covid19/mira_epitope_10_2274_LSPRWYFYY_SPRWYFYYL.tcrdist3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/mira_epitope_10_2274_LSPRWYFYY_SPRWYFYYL.tcrdist3.csv -------------------------------------------------------------------------------- /tcrdist/data/covid19/mira_epitope_110_148_ELIRQGTDY_QELIRQGTDY_QELIRQGTDYKHW.tcrdist3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/mira_epitope_110_148_ELIRQGTDY_QELIRQGTDY_QELIRQGTDYKHW.tcrdist3.csv -------------------------------------------------------------------------------- /tcrdist/data/covid19/mira_epitope_111_146_AEIPKEEVKPF_ASKIITLKK_SASKIITLK.tcrdist3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/mira_epitope_111_146_AEIPKEEVKPF_ASKIITLKK_SASKIITLK.tcrdist3.csv -------------------------------------------------------------------------------- /tcrdist/data/covid19/mira_epitope_118_136_ALNTPKDHI_ATEGALNTPK.tcrdist3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/mira_epitope_118_136_ALNTPKDHI_ATEGALNTPK.tcrdist3.csv -------------------------------------------------------------------------------- /tcrdist/data/covid19/mira_epitope_133_102_NQKLIANQF.tcrdist3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/mira_epitope_133_102_NQKLIANQF.tcrdist3.csv -------------------------------------------------------------------------------- /tcrdist/data/covid19/mira_epitope_140_92_NSSPDDQIGY_NTNSSPDDQIGYY_SSPDDQIGY_SSPDDQIGYY.tcrdist3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/mira_epitope_140_92_NSSPDDQIGY_NTNSSPDDQIGYY_SSPDDQIGY_SSPDDQIGYY.tcrdist3.csv -------------------------------------------------------------------------------- /tcrdist/data/covid19/mira_epitope_147_73_DLFMRIFTI_MDLFMRIFTI.tcrdist3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/mira_epitope_147_73_DLFMRIFTI_MDLFMRIFTI.tcrdist3.csv -------------------------------------------------------------------------------- /tcrdist/data/covid19/mira_epitope_155_59_RARSVSPKL_SVSPKLFIR.tcrdist3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/mira_epitope_155_59_RARSVSPKL_SVSPKLFIR.tcrdist3.csv -------------------------------------------------------------------------------- /tcrdist/data/covid19/mira_epitope_16_1683_QYIKWPWYI_YEQYIKWPW_YEQYIKWPWY.tcrdist3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/mira_epitope_16_1683_QYIKWPWYI_YEQYIKWPW_YEQYIKWPWY.tcrdist3.csv -------------------------------------------------------------------------------- /tcrdist/data/covid19/mira_epitope_176_44_SSTFNVPMEKLK.tcrdist3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/mira_epitope_176_44_SSTFNVPMEKLK.tcrdist3.csv -------------------------------------------------------------------------------- /tcrdist/data/covid19/mira_epitope_183_39_RIRGGDGKM_RIRGGDGKMK.tcrdist3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/mira_epitope_183_39_RIRGGDGKM_RIRGGDGKMK.tcrdist3.csv -------------------------------------------------------------------------------- /tcrdist/data/covid19/mira_epitope_185_39_ASQRVAGDSGFAAY_DSGFAAYSR_VAGDSGFAAY.tcrdist3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/mira_epitope_185_39_ASQRVAGDSGFAAY_DSGFAAYSR_VAGDSGFAAY.tcrdist3.csv -------------------------------------------------------------------------------- /tcrdist/data/covid19/mira_epitope_18_1578_FPNITNLCPF_QPTESIVRF_RFPNITNLCPF_TESIVRFPNI_VQPTESIVRF_VRFPNITNL.tcrdist3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/mira_epitope_18_1578_FPNITNLCPF_QPTESIVRF_RFPNITNLCPF_TESIVRFPNI_VQPTESIVRF_VRFPNITNL.tcrdist3.csv -------------------------------------------------------------------------------- /tcrdist/data/covid19/mira_epitope_192_31_FQPTNGVGY.tcrdist3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/mira_epitope_192_31_FQPTNGVGY.tcrdist3.csv -------------------------------------------------------------------------------- /tcrdist/data/covid19/mira_epitope_1_8260_HTTDPSFLGRY.tcrdist3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/mira_epitope_1_8260_HTTDPSFLGRY.tcrdist3.csv -------------------------------------------------------------------------------- /tcrdist/data/covid19/mira_epitope_29_1097_TVLSFCAFA_VLSFCAFAV.tcrdist3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/mira_epitope_29_1097_TVLSFCAFA_VLSFCAFAV.tcrdist3.csv -------------------------------------------------------------------------------- /tcrdist/data/covid19/mira_epitope_30_1064_KAYNVTQAF.tcrdist3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/mira_epitope_30_1064_KAYNVTQAF.tcrdist3.csv -------------------------------------------------------------------------------- /tcrdist/data/covid19/mira_epitope_37_818_FGEVFNATRF_FNATRFASVY_GEVFNATRF_NATRFASVY.tcrdist3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/mira_epitope_37_818_FGEVFNATRF_FNATRFASVY_GEVFNATRF_NATRFASVY.tcrdist3.csv -------------------------------------------------------------------------------- /tcrdist/data/covid19/mira_epitope_44_697_FPPTSFGPL.tcrdist3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/mira_epitope_44_697_FPPTSFGPL.tcrdist3.csv -------------------------------------------------------------------------------- /tcrdist/data/covid19/mira_epitope_45_689_SYFTSDYYQL_VLHSYFTSDY_YFTSDYYQLY.tcrdist3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/mira_epitope_45_689_SYFTSDYYQL_VLHSYFTSDY_YFTSDYYQLY.tcrdist3.csv -------------------------------------------------------------------------------- /tcrdist/data/covid19/mira_epitope_48_610_YLQPRTFL_YLQPRTFLL_YYVGYLQPRTF.tcrdist3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/mira_epitope_48_610_YLQPRTFL_YLQPRTFLL_YYVGYLQPRTF.tcrdist3.csv -------------------------------------------------------------------------------- /tcrdist/data/covid19/mira_epitope_51_546_AYKTFPPTEPK_KTFPPTEPK.tcrdist3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/mira_epitope_51_546_AYKTFPPTEPK_KTFPPTEPK.tcrdist3.csv -------------------------------------------------------------------------------- /tcrdist/data/covid19/mira_epitope_53_532_NYLYRLFRK_NYNYLYRLF.tcrdist3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/mira_epitope_53_532_NYLYRLFRK_NYNYLYRLF.tcrdist3.csv -------------------------------------------------------------------------------- /tcrdist/data/covid19/mira_epitope_55_524_ALRKVPTDNYITTY_KVPTDNYITTY.tcrdist3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/mira_epitope_55_524_ALRKVPTDNYITTY_KVPTDNYITTY.tcrdist3.csv -------------------------------------------------------------------------------- /tcrdist/data/covid19/mira_epitope_55_524_ALRKVPTDNYITTY_KVPTDNYITTY.tcrdist3.csv.bE5ctrl.centers.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/mira_epitope_55_524_ALRKVPTDNYITTY_KVPTDNYITTY.tcrdist3.csv.bE5ctrl.centers.csv -------------------------------------------------------------------------------- /tcrdist/data/covid19/mira_epitope_55_524_ALRKVPTDNYITTY_KVPTDNYITTY.tcrdist3.csv.bE5ctrl.centers.csv.ranked_centers.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/mira_epitope_55_524_ALRKVPTDNYITTY_KVPTDNYITTY.tcrdist3.csv.bE5ctrl.centers.csv.ranked_centers.tsv -------------------------------------------------------------------------------- /tcrdist/data/covid19/mira_epitope_55_524_ALRKVPTDNYITTY_KVPTDNYITTY.tcrdist3.radius.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/mira_epitope_55_524_ALRKVPTDNYITTY_KVPTDNYITTY.tcrdist3.radius.csv -------------------------------------------------------------------------------- /tcrdist/data/covid19/mira_epitope_67_382_APHGVVFL_APHGVVFLHV_GVVFLHVTY_VVFLHVTYV.tcrdist3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/mira_epitope_67_382_APHGVVFL_APHGVVFLHV_GVVFLHVTY_VVFLHVTYV.tcrdist3.csv -------------------------------------------------------------------------------- /tcrdist/data/covid19/mira_epitope_70_345_DTDFVNEFYAY_NRDVDTDFVNEFY.tcrdist3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/mira_epitope_70_345_DTDFVNEFYAY_NRDVDTDFVNEFY.tcrdist3.csv -------------------------------------------------------------------------------- /tcrdist/data/covid19/mira_epitope_90_216_GYQPYRVVVL_PYRVVVLSF_QPYRVVVL_QPYRVVVLSF.tcrdist3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/mira_epitope_90_216_GYQPYRVVVL_PYRVVVLSF_QPYRVVVL_QPYRVVVLSF.tcrdist3.csv -------------------------------------------------------------------------------- /tcrdist/data/covid19/mira_epitope_99_191_QECVRGTTVL.tcrdist3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/mira_epitope_99_191_QECVRGTTVL.tcrdist3.csv -------------------------------------------------------------------------------- /tcrdist/data/covid19/mira_epitope_9_2477_FLQSINFVR_FLQSINFVRI_FLYLYALVYF_GLEAPFLYLY_INFVRIIMR_LQSINFVRI_LQSINFVRII_QSINFVRII_SINFVRIIMR_VYFLQSINF_VYFLQSINFV_YFLQSINFVR_YLYALVYFL.tcrdist3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/covid19/mira_epitope_9_2477_FLQSINFVR_FLQSINFVRI_FLYLYALVYF_GLEAPFLYLY_INFVRIIMR_LQSINFVRI_LQSINFVRII_QSINFVRII_SINFVRIIMR_VYFLQSINF_VYFLQSINFV_YFLQSINFVR_YLYALVYFL.tcrdist3.csv -------------------------------------------------------------------------------- /tcrdist/data/formats/vdj.M_15_CD8_alpha.clonotypes.TRA.txt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/formats/vdj.M_15_CD8_alpha.clonotypes.TRA.txt.gz -------------------------------------------------------------------------------- /tcrdist/data/formats/vdj.M_15_CD8_beta.clonotypes.TRB.txt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/data/formats/vdj.M_15_CD8_beta.clonotypes.TRB.txt.gz -------------------------------------------------------------------------------- /tcrdist/db/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tcrdist/db/adaptive_imgt_mapping.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/db/adaptive_imgt_mapping.csv -------------------------------------------------------------------------------- /tcrdist/db/alphabeta_gammadelta_db.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/db/alphabeta_gammadelta_db.tsv -------------------------------------------------------------------------------- /tcrdist/db/combo_db.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/db/combo_db.tsv -------------------------------------------------------------------------------- /tcrdist/db/combo_xcr_2023-12-30.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/db/combo_xcr_2023-12-30.tsv -------------------------------------------------------------------------------- /tcrdist/db/combo_xcr_2024-03-05.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/db/combo_xcr_2024-03-05.tsv -------------------------------------------------------------------------------- /tcrdist/default_models/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tcrdist/default_models/human_B_heavy/J_gene_CDR3_anchors.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/default_models/human_B_heavy/J_gene_CDR3_anchors.csv -------------------------------------------------------------------------------- /tcrdist/default_models/human_B_heavy/V_gene_CDR3_anchors.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/default_models/human_B_heavy/V_gene_CDR3_anchors.csv -------------------------------------------------------------------------------- /tcrdist/default_models/human_B_heavy/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tcrdist/default_models/human_B_heavy/model_marginals.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/default_models/human_B_heavy/model_marginals.txt -------------------------------------------------------------------------------- /tcrdist/default_models/human_B_heavy/model_params.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/default_models/human_B_heavy/model_params.txt -------------------------------------------------------------------------------- /tcrdist/default_models/human_T_alpha/J_gene_CDR3_anchors.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/default_models/human_T_alpha/J_gene_CDR3_anchors.csv -------------------------------------------------------------------------------- /tcrdist/default_models/human_T_alpha/V_gene_CDR3_anchors.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/default_models/human_T_alpha/V_gene_CDR3_anchors.csv -------------------------------------------------------------------------------- /tcrdist/default_models/human_T_alpha/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tcrdist/default_models/human_T_alpha/model_marginals.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/default_models/human_T_alpha/model_marginals.txt -------------------------------------------------------------------------------- /tcrdist/default_models/human_T_alpha/model_params.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/default_models/human_T_alpha/model_params.txt -------------------------------------------------------------------------------- /tcrdist/default_models/human_T_beta/J_gene_CDR3_anchors.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/default_models/human_T_beta/J_gene_CDR3_anchors.csv -------------------------------------------------------------------------------- /tcrdist/default_models/human_T_beta/V_gene_CDR3_anchors.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/default_models/human_T_beta/V_gene_CDR3_anchors.csv -------------------------------------------------------------------------------- /tcrdist/default_models/human_T_beta/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tcrdist/default_models/human_T_beta/model_marginals.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/default_models/human_T_beta/model_marginals.txt -------------------------------------------------------------------------------- /tcrdist/default_models/human_T_beta/model_params.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/default_models/human_T_beta/model_params.txt -------------------------------------------------------------------------------- /tcrdist/default_models/mouse_T_alpha/J_gene_CDR3_anchors.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/default_models/mouse_T_alpha/J_gene_CDR3_anchors.csv -------------------------------------------------------------------------------- /tcrdist/default_models/mouse_T_alpha/V_gene_CDR3_anchors.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/default_models/mouse_T_alpha/V_gene_CDR3_anchors.csv -------------------------------------------------------------------------------- /tcrdist/default_models/mouse_T_alpha/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /tcrdist/default_models/mouse_T_alpha/model_marginals.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/default_models/mouse_T_alpha/model_marginals.txt -------------------------------------------------------------------------------- /tcrdist/default_models/mouse_T_alpha/model_params.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/default_models/mouse_T_alpha/model_params.txt -------------------------------------------------------------------------------- /tcrdist/default_models/mouse_T_beta/J_gene_CDR3_anchors.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/default_models/mouse_T_beta/J_gene_CDR3_anchors.csv -------------------------------------------------------------------------------- /tcrdist/default_models/mouse_T_beta/V_gene_CDR3_anchors.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/default_models/mouse_T_beta/V_gene_CDR3_anchors.csv -------------------------------------------------------------------------------- /tcrdist/default_models/mouse_T_beta/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tcrdist/default_models/mouse_T_beta/model_marginals.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/default_models/mouse_T_beta/model_marginals.txt -------------------------------------------------------------------------------- /tcrdist/default_models/mouse_T_beta/model_params.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/default_models/mouse_T_beta/model_params.txt -------------------------------------------------------------------------------- /tcrdist/diversity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/diversity.py -------------------------------------------------------------------------------- /tcrdist/ecdf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/ecdf.py -------------------------------------------------------------------------------- /tcrdist/gene_pairing_plot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/gene_pairing_plot.py -------------------------------------------------------------------------------- /tcrdist/html_colors.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/html_colors.py -------------------------------------------------------------------------------- /tcrdist/join.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/join.py -------------------------------------------------------------------------------- /tcrdist/mappers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/mappers.py -------------------------------------------------------------------------------- /tcrdist/memory.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/memory.py -------------------------------------------------------------------------------- /tcrdist/neighbors.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/neighbors.py -------------------------------------------------------------------------------- /tcrdist/olga_directed.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/olga_directed.py -------------------------------------------------------------------------------- /tcrdist/olga_load_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/olga_load_model.py -------------------------------------------------------------------------------- /tcrdist/paths.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/paths.py -------------------------------------------------------------------------------- /tcrdist/pgen.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/pgen.py -------------------------------------------------------------------------------- /tcrdist/plotting.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/plotting.py -------------------------------------------------------------------------------- /tcrdist/public.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/public.py -------------------------------------------------------------------------------- /tcrdist/regex.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/regex.py -------------------------------------------------------------------------------- /tcrdist/rep_diff.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/rep_diff.py -------------------------------------------------------------------------------- /tcrdist/rep_funcs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/rep_funcs.py -------------------------------------------------------------------------------- /tcrdist/repertoire.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/repertoire.py -------------------------------------------------------------------------------- /tcrdist/repertoire_db.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/repertoire_db.py -------------------------------------------------------------------------------- /tcrdist/sample.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/sample.py -------------------------------------------------------------------------------- /tcrdist/setup_tests.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/setup_tests.py -------------------------------------------------------------------------------- /tcrdist/sparse.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/sparse.py -------------------------------------------------------------------------------- /tcrdist/speed.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/speed.py -------------------------------------------------------------------------------- /tcrdist/summarize.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/summarize.py -------------------------------------------------------------------------------- /tcrdist/swap_gene_name.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/swap_gene_name.py -------------------------------------------------------------------------------- /tcrdist/tabulate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tabulate.py -------------------------------------------------------------------------------- /tcrdist/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tcrdist/tests/longtest_pgen_parallel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/longtest_pgen_parallel.py -------------------------------------------------------------------------------- /tcrdist/tests/longtest_simulate_cdr3_w_olga.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/longtest_simulate_cdr3_w_olga.py -------------------------------------------------------------------------------- /tcrdist/tests/test_automatic.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_automatic.py -------------------------------------------------------------------------------- /tcrdist/tests/test_background.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_background.py -------------------------------------------------------------------------------- /tcrdist/tests/test_breadth.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_breadth.py -------------------------------------------------------------------------------- /tcrdist/tests/test_bulkdata.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_bulkdata.py -------------------------------------------------------------------------------- /tcrdist/tests/test_centers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_centers.py -------------------------------------------------------------------------------- /tcrdist/tests/test_diversity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_diversity.py -------------------------------------------------------------------------------- /tcrdist/tests/test_downloads.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_downloads.py -------------------------------------------------------------------------------- /tcrdist/tests/test_ecdf_example.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_ecdf_example.py -------------------------------------------------------------------------------- /tcrdist/tests/test_example_1.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_example_1.py -------------------------------------------------------------------------------- /tcrdist/tests/test_example_10.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_example_10.py -------------------------------------------------------------------------------- /tcrdist/tests/test_example_11.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_example_11.py -------------------------------------------------------------------------------- /tcrdist/tests/test_example_12.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_example_12.py -------------------------------------------------------------------------------- /tcrdist/tests/test_example_13.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_example_13.py -------------------------------------------------------------------------------- /tcrdist/tests/test_example_14.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_example_14.py -------------------------------------------------------------------------------- /tcrdist/tests/test_example_15.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_example_15.py -------------------------------------------------------------------------------- /tcrdist/tests/test_example_16.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_example_16.py -------------------------------------------------------------------------------- /tcrdist/tests/test_example_17.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_example_17.py -------------------------------------------------------------------------------- /tcrdist/tests/test_example_18.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_example_18.py -------------------------------------------------------------------------------- /tcrdist/tests/test_example_19.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_example_19.py -------------------------------------------------------------------------------- /tcrdist/tests/test_example_2.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_example_2.py -------------------------------------------------------------------------------- /tcrdist/tests/test_example_20.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_example_20.py -------------------------------------------------------------------------------- /tcrdist/tests/test_example_21.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_example_21.py -------------------------------------------------------------------------------- /tcrdist/tests/test_example_22.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_example_22.py -------------------------------------------------------------------------------- /tcrdist/tests/test_example_23.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_example_23.py -------------------------------------------------------------------------------- /tcrdist/tests/test_example_24_centers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_example_24_centers.py -------------------------------------------------------------------------------- /tcrdist/tests/test_example_3.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_example_3.py -------------------------------------------------------------------------------- /tcrdist/tests/test_example_4.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_example_4.py -------------------------------------------------------------------------------- /tcrdist/tests/test_example_5.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_example_5.py -------------------------------------------------------------------------------- /tcrdist/tests/test_example_6.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_example_6.py -------------------------------------------------------------------------------- /tcrdist/tests/test_example_7.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_example_7.py -------------------------------------------------------------------------------- /tcrdist/tests/test_example_8.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_example_8.py -------------------------------------------------------------------------------- /tcrdist/tests/test_example_9.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_example_9.py -------------------------------------------------------------------------------- /tcrdist/tests/test_gallery_hdiff.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_gallery_hdiff.py -------------------------------------------------------------------------------- /tcrdist/tests/test_introduction_1.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_introduction_1.py -------------------------------------------------------------------------------- /tcrdist/tests/test_introduction_2.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_introduction_2.py -------------------------------------------------------------------------------- /tcrdist/tests/test_introduction_3.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_introduction_3.py -------------------------------------------------------------------------------- /tcrdist/tests/test_introduction_4.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_introduction_4.py -------------------------------------------------------------------------------- /tcrdist/tests/test_introduction_5.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_introduction_5.py -------------------------------------------------------------------------------- /tcrdist/tests/test_introduction_6.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_introduction_6.py -------------------------------------------------------------------------------- /tcrdist/tests/test_join.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_join.py -------------------------------------------------------------------------------- /tcrdist/tests/test_memory.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_memory.py -------------------------------------------------------------------------------- /tcrdist/tests/test_neighbors.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_neighbors.py -------------------------------------------------------------------------------- /tcrdist/tests/test_olga_synthetic.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_olga_synthetic.py -------------------------------------------------------------------------------- /tcrdist/tests/test_out_of_memory_features.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_out_of_memory_features.py -------------------------------------------------------------------------------- /tcrdist/tests/test_pgen_1.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_pgen_1.py -------------------------------------------------------------------------------- /tcrdist/tests/test_pgen_mouse.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_pgen_mouse.py -------------------------------------------------------------------------------- /tcrdist/tests/test_public.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_public.py -------------------------------------------------------------------------------- /tcrdist/tests/test_regex.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_regex.py -------------------------------------------------------------------------------- /tcrdist/tests/test_rep_funcs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_rep_funcs.py -------------------------------------------------------------------------------- /tcrdist/tests/test_repertoire.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_repertoire.py -------------------------------------------------------------------------------- /tcrdist/tests/test_repertoire_db.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_repertoire_db.py -------------------------------------------------------------------------------- /tcrdist/tests/test_rhesus.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_rhesus.py -------------------------------------------------------------------------------- /tcrdist/tests/test_setup_tests.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_setup_tests.py -------------------------------------------------------------------------------- /tcrdist/tests/test_sparse_pwrect.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_sparse_pwrect.py -------------------------------------------------------------------------------- /tcrdist/tests/test_summarize.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_summarize.py -------------------------------------------------------------------------------- /tcrdist/tests/test_translation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_translation.py -------------------------------------------------------------------------------- /tcrdist/tests/test_tree.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_tree.py -------------------------------------------------------------------------------- /tcrdist/tests/test_vdj_funcs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_vdj_funcs.py -------------------------------------------------------------------------------- /tcrdist/tests/test_workflow_1.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_workflow_1.py -------------------------------------------------------------------------------- /tcrdist/tests/test_workflow_2.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tests/test_workflow_2.py -------------------------------------------------------------------------------- /tcrdist/translation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/translation.py -------------------------------------------------------------------------------- /tcrdist/tree.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/tree.py -------------------------------------------------------------------------------- /tcrdist/vdjtools_funcs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kmayerb/tcrdist3/HEAD/tcrdist/vdjtools_funcs.py --------------------------------------------------------------------------------