{ "format": "oscr-script-manifest/1", "repository": "github.com/deeprob/bmi_monogenic", "url": "https://github.com/deeprob/BMI_monogenic", "host": "github.com", "commit": "f1e53ba154c0df9be85d57cb4260ebacda79ed5b", "license": "MIT", "license_confirmed_by": "license file LICENSE.md", "redistribution": "yes", "files": [ { "path": "LICENSE.md", "sha256": "9df98623a5d21678dd7fb01de42f8b32781928addb1dbbc0dc730aaea9bdc0a1", "language": "License", "lines": 21, "truncated": false, "block": 17, "row": 7816 }, { "path": "README.md", "sha256": "6d5ca631ac0d49c3275dfa78df25f1efb590a06bc2002fda6f51481546782d45", "language": "Text", "lines": 128, "truncated": false, "block": 18, "row": 11149 }, { "path": "notebooks/0_all_gene_forestplot.ipynb", "sha256": "f59de08a2924600fe6c2c6f3f3b0da157910e1683fba29fd0d54c210b4a60343", "language": "Jupyter", "lines": 209, "truncated": false, "block": 17, "row": 6316 }, { "path": "notebooks/10_known_gene_sex_strat_forestplot.ipynb", "sha256": "b05d14bcec1b195eb93b42767fc82efb56058137e6bc8717d5492f45ffaeeb2c", "language": "Jupyter", "lines": 86, "truncated": false, "block": 17, "row": 5583 }, { "path": "notebooks/11_supplementary_tables.ipynb", "sha256": "b5321b249456a49d0f9cfbcad0ed947474a8dbc3a55f5cece6b9f27aab92bc55", "language": "Jupyter", "lines": 216, "truncated": false, "block": 17, "row": 6378 }, { "path": "notebooks/1_per_ancestry_forestplot.ipynb", "sha256": "10f8c9f0d96bb91087df60b5fe0984ba4af6341d00f3dc6a8a1fd143019f6c63", "language": "Jupyter", "lines": 306, "truncated": false, "block": 17, "row": 6683 }, { "path": "notebooks/2_study_specific_qq_plots.ipynb", "sha256": "a5c9037e9845a781fa789230ee7525b94f3c567e33970ad98b75a258279b0093", "language": "Jupyter", "lines": 135, "truncated": false, "block": 17, "row": 5932 }, { "path": "notebooks/3_metal_statistics.ipynb", "sha256": "a0676c29a3e159e449be43f395bdd0b5b0d68fbf857031db641bc143eaff4ef6", "language": "Jupyter", "lines": 88, "truncated": false, "block": 17, "row": 5722 }, { "path": "notebooks/4_bmi_cat_enrichment.ipynb", "sha256": "e3e2191f1b7caaa4a55b314580dbec9392b3b53224e139071c396daedc1caf43", "language": "Jupyter", "lines": 161, "truncated": false, "block": 17, "row": 6179 }, { "path": "notebooks/5_comorbidity_enrichment.ipynb", "sha256": "57c9fbe1e5399725cd2f57069a6b0db3680314dfcb824d93ed8b9f0739d74f2d", "language": "Jupyter", "lines": 105, "truncated": false, "block": 17, "row": 5769 }, { "path": "notebooks/6_phewas_manhattan.R", "sha256": "c60a7a52bbf79560a88bcbe0983ca2af2a159629a2735d5925a1a1ae83f7cef9", "language": "R", "lines": 23, "truncated": false, "block": 18, "row": 6167 }, { "path": "notebooks/7_pgs_interaction.ipynb", "sha256": "5209f0b3fa8fb970ce3cb9cc0fbc82c4faf72993121d0d8c50bbfafb49674d86", "language": "Jupyter", "lines": 247, "truncated": false, "block": 17, "row": 6442 }, { "path": "notebooks/8_proteomics.ipynb", "sha256": "6b1ddca786d7cc97c22dadf2d96e84379ffbbe4676d5b57cef5a1661fe1c1184", "language": "Jupyter", "lines": 239, "truncated": false, "block": 17, "row": 6432 }, { "path": "notebooks/9_known_gene_forestplot.ipynb", "sha256": "65af0fbba211be05e4abd6c01812f80a759725f1358b984c15d30022dee159d2", "language": "Jupyter", "lines": 82, "truncated": false, "block": 17, "row": 5601 }, { "path": "notebooks/plotting.py", "sha256": "8ea5f124ef996e76c037d0b4dd4d45edc829d1badad661fc1ec0a97ca3f70f6a", "language": "Python", "lines": 146, "truncated": false, "block": 17, "row": 29890 }, { "path": "notebooks/tables.py", "sha256": "4a10de48b28da0eb8ce8e0201a3d88ad4c9c151dd4dae2fb6bc01440493259f2", "language": "Python", "lines": 93, "truncated": false, "block": 17, "row": 28198 }, { "path": "src/ancestry_inference/dnanexus_notebooks/ancestry_inference.ipynb", "sha256": "eb1f735e2a86359d075535c71b3923da3fd728e5f71853085aac5623f0d17561", "language": "Jupyter", "lines": 184, "truncated": false, "block": 17, "row": 5961 }, { "path": "src/ancestry_inference/dnanexus_notebooks/pca_computation.ipynb", "sha256": "1b4894a62362a1978586d14f2d35b5db38c34c52d97c21ad68f476e419c9aaae", "language": "Jupyter", "lines": 422, "truncated": false, "block": 17, "row": 6413 }, { "path": "src/ancestry_inference/dnanexus_notebooks/pca_computation_ni.ipynb", "sha256": "58401ba408539123d8b43c950d386d3851fb3674b8661dfba56b0d602e8f3aad", "language": "Jupyter", "lines": 154, "truncated": false, "block": 17, "row": 5759 }, { "path": "src/ancestry_inference/dnanexus_notebooks/sample_qc.ipynb", "sha256": "515907e3871a8365b50fabdd31c24a232fcfef2ab5b7f35509f0a37a28722c73", "language": "Jupyter", "lines": 88, "truncated": false, "block": 17, "row": 5505 }, { "path": "src/downstream/0_process_meta_files.py", "sha256": "0f7da37fa0e8a4abaec5ceb9de831287b10b3b71ab77fa6d77d1957927b8922d", "language": "Python", "lines": 34, "truncated": false, "block": 17, "row": 22309 }, { "path": "src/downstream/1_conduct_meta_analysis.py", "sha256": "9c11e34fb0d264b604eb0ae9cd43f30f31b1663ffb16bcfa7bb07738523eca7c", "language": "Python", "lines": 34, "truncated": false, "block": 17, "row": 22160 }, { "path": "src/downstream/2_create_meta_files.py", "sha256": "9e1ac6f0100f3a5200165f497700caa8c89ff238703a13a0a9b3147e6e988641", "language": "Python", "lines": 35, "truncated": false, "block": 17, "row": 21886 }, { "path": "src/downstream/3_enrichment_cat.py", "sha256": "344133e6c04a2cb12584b41e826da8aca8a02f915ddb24fe023b3d76b73dad3d", "language": "Python", "lines": 79, "truncated": false, "block": 17, "row": 26660 }, { "path": "src/downstream/4_sem.py", "sha256": "02a8ed4a002a5a89f9e38a3791a123bb0fc60c2678b818d1c7e121e623e25a50", "language": "Python", "lines": 62, "truncated": false, "block": 17, "row": 24157 }, { "path": "src/downstream/5_phewas.py", "sha256": "d782e2fff7df8f7d2dab1e9f4859cfdd9ca7c7f85a4b12aa1212049a5ba8da40", "language": "Python", "lines": 140, "truncated": false, "block": 17, "row": 30685 }, { "path": "src/downstream/6_add_nvariants_to_meta.py", "sha256": "93b89d31fd6ce53331da2c56539d861c9f35a583987a87a7a996d37a0527cc35", "language": "Python", "lines": 50, "truncated": false, "block": 17, "row": 23633 }, { "path": "src/downstream/dnanexus_notebooks/10a_shadow_effect_nearby_common_variants.ipynb", "sha256": "352b9a64216b6b5c43268b8aecf40e870aebccd9cff23eaa812709db72a7aaa7", "language": "Jupyter", "lines": 185, "truncated": false, "block": 17, "row": 6175 }, { "path": "src/downstream/dnanexus_notebooks/11a_medication_extract_data.ipynb", "sha256": "6f9e8d5e940868cfb90ff655a703ce8e1fdccf058376b1eb6a3f1287388c34c1", "language": "Jupyter", "lines": 82, "truncated": false, "block": 17, "row": 5534 }, { "path": "src/downstream/dnanexus_notebooks/11b_medication_prepare_pheno.ipynb", "sha256": "f83e2456c462920d941182d31b7efbd7c369e58e96f546bccdebc73734943eb5", "language": "Jupyter", "lines": 57, "truncated": false, "block": 17, "row": 5557 }, { "path": "src/downstream/dnanexus_notebooks/12a_enrichment_obesity_category.ipynb", "sha256": "e013c20c7b7b68139415086f2554586e47df3343d9668a5a3042fe8b2ad19fbe", "language": "Jupyter", "lines": 159, "truncated": false, "block": 17, "row": 6074 }, { "path": "src/downstream/dnanexus_notebooks/12b_enrichment_obesity_comorbidity.ipynb", "sha256": "7fb603c6d8ce9369710e66ff85e2c9fbb6230e7ad8c820a6fb1894f402cae27b", "language": "Jupyter", "lines": 131, "truncated": false, "block": 17, "row": 5999 }, { "path": "src/downstream/dnanexus_notebooks/12c_phewas_map_samples_to_phecodes.ipynb", "sha256": "3bc86f257d6dac07715612e542cbe0647a8eb1798666b3b9034edee215ea45ec", "language": "Jupyter", "lines": 105, "truncated": false, "block": 17, "row": 5559 }, { "path": "src/downstream/dnanexus_notebooks/12d_phewas_run.ipynb", "sha256": "1f2e41f189fcee6eb741263f7c4991e5ba20da9a03d82e2e60f9d003039567ec", "language": "Jupyter", "lines": 201, "truncated": false, "block": 17, "row": 6141 }, { "path": "src/downstream/dnanexus_notebooks/12e_sem_conduct.ipynb", "sha256": "8c6bb4a22c841010278f799801ea163bac44767725be7eb6e3c1695631b86b49", "language": "Jupyter", "lines": 288, "truncated": false, "block": 17, "row": 6356 }, { "path": "src/downstream/dnanexus_notebooks/13b_pgs_interaction.ipynb", "sha256": "342b14e27e10b97851038cfda3190f4024adf666262f41f2a046187d9069b15b", "language": "Jupyter", "lines": 146, "truncated": false, "block": 17, "row": 6108 }, { "path": "src/downstream/dnanexus_notebooks/14a_proteomics_protein_assoc.ipynb", "sha256": "7121247e225094e3552b003626a99cfde2941cb00d70f7f742718bc5fb7ecbbb", "language": "Jupyter", "lines": 239, "truncated": false, "block": 17, "row": 6363 }, { "path": "src/downstream/dnanexus_notebooks/14b_proteomics_bmi_assoc.ipynb", "sha256": "c07282c8820036a65016d53fa6c8f3be137c373b661f43ad95dc04de80373736", "language": "Jupyter", "lines": 190, "truncated": false, "block": 17, "row": 6010 }, { "path": "src/downstream/download_hgnc.sh", "sha256": "dc30552897571a269d1edeebe34893e68308844faf79794ffc324dfc65b4f64a", "language": "Shell", "lines": 1, "truncated": false, "block": 18, "row": 8735 }, { "path": "src/downstream/run_proteomics_protein_assoc.sh", "sha256": "b294aed5bc6e5ded1aa43f58d3ab3339171518f95fdc66658b4e140a9158e86b", "language": "Shell", "lines": 17, "truncated": false, "block": 18, "row": 9011 }, { "path": "src/downstream/utils/meta.py", "sha256": "9adf0294eda649d1619853dbf37d3ca464ac6c4e921774d8ee3cc245dfdcab7c", "language": "Python", "lines": 452, "truncated": false, "block": 18, "row": 3855 }, { "path": "src/gene_burden_association_tests/1_run_regenie_step1.sh", "sha256": "c2daa12f43a505142dc864caaeb8faf6006b0cd1735f23f6da32c5dba6af2794", "language": "Shell", "lines": 11, "truncated": false, "block": 18, "row": 8799 }, { "path": "src/gene_burden_association_tests/1_run_regenie_step1_quant_helper.sh", "sha256": "ad5215e12c506099618a69b8276347abeba827b0e78f82797c05d4d84560fea7", "language": "Shell", "lines": 46, "truncated": false, "block": 18, "row": 9783 }, { "path": "src/gene_burden_association_tests/2_run_regenie_step2.sh", "sha256": "ef9b47ca48de511f488d0d1ab782ae5ec7fa95ca1ccaeb5d938ceddf880aa694", "language": "Shell", "lines": 17, "truncated": false, "block": 18, "row": 8944 }, { "path": "src/gene_burden_association_tests/2_run_regenie_step2_quant_helper.sh", "sha256": "c47179917647f0c3938f1b0b9a7e769b14911beeb791d3ad2da51d19667dcd17", "language": "Shell", "lines": 66, "truncated": false, "block": 18, "row": 9958 }, { "path": "src/genetic_data_processing/burden_preparation/dnanexus_notebooks/0_prepare_burden_file.ipynb", "sha256": "9757146e04442e7641f7167ae63ac44a3331ebb3d6f32466f32f00affd4a9783", "language": "Jupyter", "lines": 93, "truncated": false, "block": 17, "row": 5690 }, { "path": "src/genetic_data_processing/burden_preparation/dnanexus_notebooks/1_add_gnomad_annot.ipynb", "sha256": "6e9e50de1b3b0222e908c69cccabd75495200260384a180bf8d56ab93100c807", "language": "Jupyter", "lines": 196, "truncated": false, "block": 17, "row": 6042 }, { "path": "src/genetic_data_processing/burden_preparation/dnanexus_notebooks/2_create_assoc_files.ipynb", "sha256": "0979f90997f3c0f4600cc73396466706ff895c893b65f39ffa4d8a9281bcc491", "language": "Jupyter", "lines": 79, "truncated": false, "block": 17, "row": 5646 }, { "path": "src/genetic_data_processing/sample_qc/flag_samples/dnanexus_notebooks/chr1.ipynb", "sha256": "5578e688c0e082aa6695c1f22f47767c759cad456340677456e5db3b89fd8cab", "language": "Jupyter", "lines": 50, "truncated": false, "block": 17, "row": 5469 }, { "path": "src/genetic_data_processing/sample_qc/flag_samples/dnanexus_notebooks/flag_samples.ipynb", "sha256": "27f4292e9fb8cdf19927b7173727c7c0d6d4177a140537287441d44426a22d54", "language": "Jupyter", "lines": 188, "truncated": false, "block": 17, "row": 5922 }, { "path": "src/genetic_data_processing/sample_qc/flag_samples/dnanexus_notebooks/sample_annot.ipynb", "sha256": "df1c085afd907586400e39e57203f5436a76d999444b5b69d881c2bbae1d3d72", "language": "Jupyter", "lines": 304, "truncated": false, "block": 17, "row": 6416 }, { "path": "src/genetic_data_processing/sample_qc/flag_samples/dnanexus_notebooks/sample_qc.ipynb", "sha256": "b702f94f8e8c65596bbadd677289da7541816aff239d611de693b04c5e1c84bd", "language": "Jupyter", "lines": 200, "truncated": false, "block": 17, "row": 6095 }, { "path": "src/genetic_data_processing/sample_qc/flag_samples/run_repartition.sh", "sha256": "56c1b59f4add9daadbf3137f19292cafc42e946d4f3ec12b183cfbd14459217c", "language": "Shell", "lines": 22, "truncated": false, "block": 18, "row": 9136 }, { "path": "src/genetic_data_processing/sample_qc/flag_samples/run_sample_qc.sh", "sha256": "3661e944ef429dc3a8c7edc35f2a47f4a75b5abe01358dfc5fc0ba16124ceb8c", "language": "Shell", "lines": 21, "truncated": false, "block": 18, "row": 9063 }, { "path": "src/genetic_data_processing/sample_qc/high_quality_variants/filter_X_hqc.sh", "sha256": "4ace758dc2378db5c5f067f779909ae7b257ecd9f04865573ad0e0112c130948", "language": "Shell", "lines": 24, "truncated": false, "block": 18, "row": 9339 }, { "path": "src/genetic_data_processing/sample_qc/high_quality_variants/merge_autosome_hqc.sh", "sha256": "b83cc89dd1e57732a990138e786b1dbf3e9591a144354057c8a85d4718b0d63a", "language": "Shell", "lines": 104, "truncated": false, "block": 18, "row": 10199 }, { "path": "src/genetic_data_processing/sample_qc/high_quality_variants/merge_autosome_hqc_pruned.sh", "sha256": "70815cebd51bbe2b8b9ae4569648aee27b913b3b268972b95975b0504b72fd78", "language": "Shell", "lines": 104, "truncated": false, "block": 18, "row": 10210 }, { "path": "src/genetic_data_processing/sample_qc/high_quality_variants/run_X_hqc.sh", "sha256": "e127582d9123b46f9be557049e338a587896db27923e5537d5ce85c472146feb", "language": "Shell", "lines": 27, "truncated": false, "block": 18, "row": 9537 }, { "path": "src/genetic_data_processing/sample_qc/high_quality_variants/run_X_hqc_pruned.sh", "sha256": "34b5ce94c70f1b23ec31b41e8eeaff64be3fe6942e8517cabce2f9fc2e2bb939", "language": "Shell", "lines": 27, "truncated": false, "block": 18, "row": 9489 }, { "path": "src/genetic_data_processing/sample_qc/high_quality_variants/run_autosome_hqc.sh", "sha256": "f42380d50ebc146001272ff6af66f2117e061a659252db7587a44ddf5d0ee58e", "language": "Shell", "lines": 27, "truncated": false, "block": 18, "row": 9534 }, { "path": "src/genetic_data_processing/sample_qc/high_quality_variants/run_autosome_hqc_pruned.sh", "sha256": "3932116da8ce48a3841cb6bd718ed09798c4a65f5c39fc4741c8cb591fbf3134", "language": "Shell", "lines": 27, "truncated": false, "block": 18, "row": 9472 }, { "path": "src/genetic_data_processing/sample_qc/impute_sex/dnanexus_notebooks/impute_sex.ipynb", "sha256": "66fab5b7697e05e8827bdaff7903787af61effe59aa64770903c8c1de8ca6f0e", "language": "Jupyter", "lines": 120, "truncated": false, "block": 17, "row": 5739 }, { "path": "src/genetic_data_processing/sample_qc/relatedness/create_autosome_subsets.sh", "sha256": "24c6742ecf7853a09b932587247810bc47898a0af9cfe6a8a9a7a05656410c8f", "language": "Shell", "lines": 20, "truncated": false, "block": 18, "row": 9354 }, { "path": "src/genetic_data_processing/sample_qc/relatedness/dnanexus_notebooks/kinship.ipynb", "sha256": "91c59c2fe68ac7d4fe90a3d9f7df52a031214a6ed9826fc70f13786a7d05404d", "language": "Jupyter", "lines": 179, "truncated": false, "block": 17, "row": 5938 }, { "path": "src/genetic_data_processing/sample_qc/relatedness/get_king_estimates.sh", "sha256": "182c491c4fd61881f0387cc937c7398f82dd09797c83c4b228ae14cffd6baf71", "language": "Shell", "lines": 22, "truncated": false, "block": 18, "row": 9342 }, { "path": "src/genetic_data_processing/sample_qc/relatedness/get_king_estimates_diff_subset.sh", "sha256": "082e8f30ddf8fe975c1813a9a192a09304da1d752dc809696df974b949eec0ac", "language": "Shell", "lines": 34, "truncated": false, "block": 18, "row": 9596 }, { "path": "src/genetic_data_processing/sample_qc/relatedness/get_king_estimates_same_subset.sh", "sha256": "da203b1b5e4211b9d84b348da6bb0fd08386cc758abf71d2e8f35ae99baef77c", "language": "Shell", "lines": 25, "truncated": false, "block": 18, "row": 9384 }, { "path": "src/genetic_data_processing/snp_qc/0_qc_snp_data.sh", "sha256": "938c256145b0ad2e96657702196eedeef0478ea2f6459ff6a394247d0b5dd95c", "language": "Shell", "lines": 22, "truncated": false, "block": 18, "row": 9385 }, { "path": "src/genetic_data_processing/snp_qc/1_qc_snp_data_ld_prune.sh", "sha256": "6108b73a69f4c3e20a75e1d3a5e9ecb49b240dc36fd220953f71ff0c5573627a", "language": "Shell", "lines": 25, "truncated": false, "block": 18, "row": 9474 }, { "path": "src/genetic_data_processing/snp_qc/2_snp_anc.sh", "sha256": "50f948c891f1446f47e034f40c02dc566f2bfd7351ceec4b83b875d9c5787d00", "language": "Shell", "lines": 11, "truncated": false, "block": 18, "row": 8773 }, { "path": "src/genetic_data_processing/snp_qc/2_snp_anc_helper.sh", "sha256": "edaab02fa7883304888c86d859074212a881066bc3056d364a9233dd19c5ddb6", "language": "Shell", "lines": 28, "truncated": false, "block": 18, "row": 9527 }, { "path": "src/genetic_data_processing/variant_annot/dnanexus_notebooks/chr1.ipynb", "sha256": "1b59e19add45317e6218c23ff1097c728ecb778dabc7f9c0b3b0ca841818288f", "language": "Jupyter", "lines": 246, "truncated": false, "block": 17, "row": 6464 }, { "path": "src/genetic_data_processing/variant_annot/run_vannot.sh", "sha256": "0a348c25fa5383d59b8b2ee21200ac9d7b780ae2909139fb8380efab73cbb723", "language": "Shell", "lines": 19, "truncated": false, "block": 18, "row": 8991 }, { "path": "src/genetic_data_processing/variant_qc/dnanexus_notebooks/0_initial_variant_qc_chr1.ipynb", "sha256": "9a661346fe764102572507fe3c4c80c26fbc0cdd121db6d4d4dc5aae69d2989a", "language": "Jupyter", "lines": 114, "truncated": false, "block": 17, "row": 5783 }, { "path": "src/genetic_data_processing/variant_qc/run_vqc.sh", "sha256": "ebaed09de555e3186ec191e76a9a38cef53cb27a22d8380936c7b055a16b8d6f", "language": "Shell", "lines": 19, "truncated": false, "block": 18, "row": 9077 }, { "path": "src/phenotypic_data_processing/dnanexus_notebooks/05a_extract_bmi_and_covariate_data.ipynb", "sha256": "e72a31103df5c93a95f14c5cc03b224bcc278c1c3da43ae3927d8ac346cae397", "language": "Jupyter", "lines": 102, "truncated": false, "block": 17, "row": 5650 }, { "path": "src/phenotypic_data_processing/dnanexus_notebooks/05b_extract_icd_codes_data.ipynb", "sha256": "0f40b35234baa7f6448a1aa53eb0ef8c74126e2cfc810603c89d702867ad3c79", "language": "Jupyter", "lines": 76, "truncated": false, "block": 17, "row": 5503 }, { "path": "src/phenotypic_data_processing/dnanexus_notebooks/05c_extract_lifestyle_data.ipynb", "sha256": "166c017ae889c3ca111187e7ab4befb64cafcfa35d04397108de5619924f21c7", "language": "Jupyter", "lines": 106, "truncated": false, "block": 17, "row": 5760 }, { "path": "src/phenotypic_data_processing/dnanexus_notebooks/05d_prepare_pheno_files.ipynb", "sha256": "2d046331f1b33192331c8a95d39d3c91a185ebda58c5898df01e4801fdabefc4", "language": "Jupyter", "lines": 448, "truncated": false, "block": 17, "row": 6942 }, { "path": "src/phenotypic_data_processing/dnanexus_notebooks/05e_normalize_pheno.ipynb", "sha256": "a7ee880cea475d2e1c95cf81a88f22402964aaacd4ea774b4ff18cb9cca1bc04", "language": "Jupyter", "lines": 114, "truncated": false, "block": 17, "row": 5756 } ] }