{ "format": "oscr-script-manifest/1", "repository": "github.com/openomics/chrom-seek", "url": "https://github.com/OpenOmics/chrom-seek", "host": "github.com", "commit": "2dd4ad2b4d903975c0a76b6b12cf3e303a74831b", "license": "MIT", "license_confirmed_by": "license file LICENSE", "redistribution": "yes", "files": [ { "path": ".github/autorelease.py", "sha256": "968d6f9d1e6cd3678a3c185711724e3ad5dc388ae61e6f725dabaa54ed6bb27c", "language": "Python", "lines": 493, "truncated": false, "block": 15, "row": 23922 }, { "path": ".github/sv/snakevis.py", "sha256": "e8d4869cbf2ba2442b2d66626c57eceec19ac1d963ef74277245ed3388470402", "language": "Python", "lines": 334, "truncated": false, "block": 15, "row": 22802 }, { "path": "LICENSE", "sha256": "c4b274d22d66e950ab110dcb70108508fe49ec3002703618c2bea67a2ba33f39", "language": "License", "lines": 21, "truncated": false, "block": 11, "row": 13982 }, { "path": "README.md", "sha256": "6c18972b6b38722961f8dcd6d50bb3532179328d5d00647873dfc1df355b577b", "language": "Text", "lines": 98, "truncated": false, "block": 16, "row": 7518 }, { "path": "bin/DiffBind_PCA_normalizedCounts.R", "sha256": "17d3c9285ca383373205b17168ba4f920c2fc916d4e9243efacc00a8fe24832a", "language": "R", "lines": 180, "truncated": false, "block": 16, "row": 3170 }, { "path": "bin/DiffBind_v2_Deseq2.Rmd", "sha256": "6a0f03b43d51a89261006e3d9c8e7b0e2e80b41973f6f944057073dee59018ba", "language": "R", "lines": 221, "truncated": false, "block": 16, "row": 3242 }, { "path": "bin/DiffBind_v2_Deseq2_block.Rmd", "sha256": "986dc3bbb96dfe2948f64bca61db375c8885214da3c1f8e6d3f3de8295cae59a", "language": "R", "lines": 220, "truncated": false, "block": 16, "row": 3249 }, { "path": "bin/DiffBind_v2_EdgeR.Rmd", "sha256": "3ae7dc8ab620fd67325c5d09bd56f872dadf05d6d3bf65401172807a6fc3f550", "language": "R", "lines": 217, "truncated": false, "block": 16, "row": 3216 }, { "path": "bin/DiffBind_v2_EdgeR_block.Rmd", "sha256": "d066e814ae4a009916822cb6f8525edf28d6755037fc5783b7ec3c502e43734e", "language": "R", "lines": 220, "truncated": false, "block": 16, "row": 3233 }, { "path": "bin/DiffBind_v2_QC.Rmd", "sha256": "ce18c8b8906d0589284e8cacd44622c268a82a1d662b37374eca5d7b6943a5f8", "language": "R", "lines": 383, "truncated": false, "block": 16, "row": 3797 }, { "path": "bin/DiffBind_v2_load.R", "sha256": "04d1b854aa0b435d651dc290c4a53ec3a6f68a97cf36f0c737d603def91ab9b0", "language": "R", "lines": 84, "truncated": false, "block": 16, "row": 2608 }, { "path": "bin/bam2fragment.R", "sha256": "5e6d39e223baa8469a3c0887632e2dd433968e6b5f99d3c5f75c1a9d4ea5981e", "language": "R", "lines": 18, "truncated": false, "block": 16, "row": 1982 }, { "path": "bin/bam_filter_by_mapq.py", "sha256": "8c8cf361ef0aec5f8cf76f348758caa5bc0437a129abbea7ac16baabe4cf8a71", "language": "Python", "lines": 40, "truncated": false, "block": 15, "row": 9551 }, { "path": "bin/cfChIP_signatures.R", "sha256": "5f741d3fc04262af22a23cb0153d646fa0a4aca8a2b23c9d3b29230e2e77bb44", "language": "R", "lines": 97, "truncated": false, "block": 16, "row": 2845 }, { "path": "bin/creattable.py", "sha256": "5b4a045b19e460dc68fa6a7d37140fdcca67ee4e4284a5e883944efb3c925791", "language": "Python", "lines": 46, "truncated": false, "block": 15, "row": 9629 }, { "path": "bin/filterMetrics.py", "sha256": "6551188894a5c66bdab7d7eba755f541edb4d3a82cd03d0d2726c67c2c739d4e", "language": "Python", "lines": 113, "truncated": false, "block": 15, "row": 14702 }, { "path": "bin/frip.py", "sha256": "f437d6de08833d668680a532acd64f67605c3ca587f5ccc8f19a465dc4e2eb0b", "language": "Python", "lines": 230, "truncated": false, "block": 15, "row": 19174 }, { "path": "bin/frip_summary_plot.py", "sha256": "ed26307e7259a1f7834cf79860d16fb78a84f63cb63bc4fdbcba31d515a7d175", "language": "Python", "lines": 157, "truncated": false, "block": 15, "row": 17118 }, { "path": "bin/jaccard_score.py", "sha256": "1740a48034d409cedb56953b036d658aa77d91c1e92edb44b94c16218bc96d7f", "language": "Python", "lines": 474, "truncated": false, "block": 15, "row": 24076 }, { "path": "bin/jaccard_summary.py", "sha256": "193951dd35729787ab35a2610e5f4e93150f22a69c604f4f9995ddaa77759f51", "language": "Python", "lines": 152, "truncated": false, "block": 15, "row": 17596 }, { "path": "bin/merge_uropa_diffbind.py", "sha256": "b275e93448c0529163103fb966aaf5a7bbef75a61dd5e7536db0b4761bb7d6a9", "language": "Python", "lines": 206, "truncated": false, "block": 15, "row": 19528 }, { "path": "bin/nrf.py", "sha256": "6f78a8bf5798edb00345dd48327fec986770cf651dfdd21081771f7548c1392b", "language": "Python", "lines": 27, "truncated": false, "block": 15, "row": 7735 }, { "path": "bin/ppqt/run_spp.R", "sha256": "01b23c758856407334480d418b217b5987a232ce4a2f8cadc6aaf8ee3b33b25a", "language": "R", "lines": 887, "truncated": false, "block": 16, "row": 4298 }, { "path": "bin/ppqt/run_spp_nodups.R", "sha256": "519e21732c812a37e1b1fc5e6b0a180a6cbea71e32a0a818f26cd36fcaa7adc8", "language": "R", "lines": 886, "truncated": false, "block": 8, "row": 5065 }, { "path": "bin/ppqt_process.py", "sha256": "3cff08a1f4386847360cb27fcf1e077fe57194f2a5a2ad5186c8565aa6fddc16", "language": "Python", "lines": 32, "truncated": false, "block": 15, "row": 8011 }, { "path": "bin/prep_diffbind.py", "sha256": "b148443f41e4961061853b96a82a5714630570673b803760695472adad1683b9", "language": "Python", "lines": 65, "truncated": false, "block": 15, "row": 13377 }, { "path": "bin/prep_diffbindQC.py", "sha256": "16f35fdf9cec3be07c92e606005a09d8cce3a0f8adb6290765e6b49f6f06557a", "language": "Python", "lines": 155, "truncated": false, "block": 15, "row": 16619 }, { "path": "bin/promoterAnnotation_by_Gene.R", "sha256": "52791967af5af05805cdfbdefe7ce79630334a3fa41b98b74005a93fba569ede", "language": "R", "lines": 193, "truncated": false, "block": 16, "row": 3577 }, { "path": "bin/significantPathways.R", "sha256": "574a27ca941a509639ff9722e8ef28939f0fa1ca02a652304b30b531c5653de1", "language": "R", "lines": 127, "truncated": false, "block": 16, "row": 3145 }, { "path": "bin/summary_tables.py", "sha256": "5c7fdd7447e9798700482c6583ba5905effffbd54fab741db58aececd33e170d", "language": "Python", "lines": 258, "truncated": false, "block": 15, "row": 22274 }, { "path": "bin/uropa_input.py", "sha256": "3fdbbea2e733dca274708033d11801782081c63cd42006a5ea112ac742fc8ef7", "language": "Python", "lines": 97, "truncated": false, "block": 15, "row": 16172 }, { "path": "run_tests.sh", "sha256": "0c075cebee09cc86f316d101e9a4c0fdaf07bcf4b5e378473cbdd4bda1e4327d", "language": "Shell", "lines": 1, "truncated": false, "block": 16, "row": 4522 }, { "path": "src/__init__.py", "sha256": "5db2f3d8163e1f914cf13ce940d8d69e346dcdcec6b08722a9381c148fec9bc5", "language": "Python", "lines": 16, "truncated": false, "block": 12, "row": 4940 }, { "path": "src/cache.sh", "sha256": "ebd3eb30b310e692fed3c43826d9e16d1de105f0ba7cd496b58cb4fe263eec34", "language": "Shell", "lines": 231, "truncated": false, "block": 16, "row": 6589 }, { "path": "src/files.py", "sha256": "fa2e11cda49fea00bcc87034876ce5ab18d1acdd9840ae8e68b65eee2acb639c", "language": "Python", "lines": 476, "truncated": false, "block": 15, "row": 24312 }, { "path": "src/run.py", "sha256": "d159732ce82fcc57d19693c626a4fa79416f181189f0f0a39d2e7dab7a2bac49", "language": "Python", "lines": 839, "truncated": false, "block": 16, "row": 498 }, { "path": "src/run.sh", "sha256": "04f20146b962f44f0a7091559168c5cf0c6405b204e8406924a042829377794b", "language": "Shell", "lines": 320, "truncated": false, "block": 16, "row": 6674 }, { "path": "src/shells.py", "sha256": "5156910f8dff11cdd11eb797fff7c8835cd7bf0bad5d874f1df15d14cc60370b", "language": "Python", "lines": 70, "truncated": false, "block": 12, "row": 8983 }, { "path": "src/utils.py", "sha256": "b2195c2e418a090edbb0a5c342d6feccd05e94aa2ba0afbaac82a2eeea96acae", "language": "Python", "lines": 406, "truncated": false, "block": 15, "row": 23493 }, { "path": "tests/test_jaccard.py", "sha256": "22f3690630580c3684230e03e310862e863bcb4768182295ef17e0092214205f", "language": "Python", "lines": 437, "truncated": false, "block": 15, "row": 24717 }, { "path": "tests/test_peakcall.py", "sha256": "30c0dccb4cf5ce405d239c54c82a745408c1da2bef25e4d50559a0613af5c2d0", "language": "Python", "lines": 319, "truncated": false, "block": 15, "row": 22641 }, { "path": "tests/test_qc_guards.py", "sha256": "1080b33abd2d70663f72d582b50d3bfc8c5e3d303ba4fd30cc71565f8dfeefb2", "language": "Python", "lines": 82, "truncated": false, "block": 15, "row": 12351 }, { "path": "workflow/scripts/common.py", "sha256": "76c4d0e7cc7de50fb2ae4df417866aed2b9cc57563e504d5719922f086e19d44", "language": "Python", "lines": 241, "truncated": false, "block": 15, "row": 21025 }, { "path": "workflow/scripts/grouping.py", "sha256": "f2f98f5f080aec7e73f4ca87978c8711f29d63d92fe14ae793e8b2c08345a0c6", "language": "Python", "lines": 78, "truncated": false, "block": 15, "row": 12109 }, { "path": "workflow/scripts/peakcall.py", "sha256": "ac94f99886acdc22e6b852836dca655093468856ed70d3f15fab22b7c9ea53fa", "language": "Python", "lines": 63, "truncated": false, "block": 15, "row": 12264 }, { "path": "workflow/scripts/utils.sh", "sha256": "90713e79ed60616093dd7ee194514282a81f3054772e3e5bb0c5750076ffc797", "language": "Shell", "lines": 38, "truncated": false, "block": 13, "row": 4998 } ] }