{
 "format": "oscr-script-manifest/1",
 "repository": "github.com/saketkc/gencode_regions",
 "url": "https://github.com/saketkc/gencode_regions",
 "host": "github.com",
 "commit": "f1f169e394d41488df505e7ad34aa0688cb08262",
 "license": "BSD-2-Clause",
 "license_confirmed_by": "license file LICENSE",
 "redistribution": "yes",
 "files": [
  {
   "path": "GTF.py",
   "sha256": "f86c692f162066b564dbc6667ba31bc6f621ba7b027b844205fca2383a426658",
   "language": "Python",
   "lines": 135,
   "truncated": false,
   "block": 6,
   "row": 38311
  },
  {
   "path": "LICENSE",
   "sha256": "786b5296d229b6b38bed96d460e091b70ca589a5fffce99ab9d63a111e6248dc",
   "language": "License",
   "lines": 25,
   "truncated": false,
   "block": 6,
   "row": 1944
  },
  {
   "path": "README.md",
   "sha256": "bf023aa7abe8ac16e46f934fef0ff1105f0aa3a78ba83d12f079fb5ea728e631",
   "language": "Text",
   "lines": 116,
   "truncated": false,
   "block": 8,
   "row": 10035
  },
  {
   "path": "create_regions_from_gencode.R",
   "sha256": "fb6986f2b03d1302690725bf30cbbe330f9153eaffdc48935fb66f1209f374ab",
   "language": "R",
   "lines": 127,
   "truncated": false,
   "block": 8,
   "row": 3342
  },
  {
   "path": "create_without_rRNA_tRNA.sh",
   "sha256": "823b5e5bb4808a8a893cbbe4a33ea39a99a6d83dfaed643127d19db3d6e9c64e",
   "language": "Shell",
   "lines": 3,
   "truncated": false,
   "block": 8,
   "row": 6807
  },
  {
   "path": "extract_lincRNA.py",
   "sha256": "07af19ebcc1fbf5f81530451acb7493c1fbb2f1e06f2f34c9c58df3e0fc8ed70",
   "language": "Python",
   "lines": 31,
   "truncated": false,
   "block": 6,
   "row": 26126
  },
  {
   "path": "extract_rRNA.py",
   "sha256": "f7f0a0060dccaf392d5bd796a71a24d780ad4791a6e992618d07abaebfe803e6",
   "language": "Python",
   "lines": 33,
   "truncated": false,
   "block": 6,
   "row": 26094
  },
  {
   "path": "extract_tRNA.py",
   "sha256": "3884f5255b814bd39d98832360962f7d7c069f166dd2024ddee68c69f92ef5f9",
   "language": "Python",
   "lines": 33,
   "truncated": false,
   "block": 6,
   "row": 26086
  },
  {
   "path": "genepred_to_bed.py",
   "sha256": "664270c5f1f6f9489f8a38cc03f46c202a07ccf342404db8bdca0ffee0eca127",
   "language": "Python",
   "lines": 149,
   "truncated": false,
   "block": 6,
   "row": 40653
  },
  {
   "path": "notebooks/ASM276v2.ipynb",
   "sha256": "74dbb0eb7a5b7676903e14499dcc117164053a25f20c842f38b40c6231d15c32",
   "language": "Jupyter",
   "lines": 297,
   "truncated": false,
   "block": 6,
   "row": 57
  },
  {
   "path": "notebooks/ASM294v2.ipynb",
   "sha256": "482c5d85c4c5e6fe6a33903405d84aa8661d5f471de8714eb5c2c9f3355c1e53",
   "language": "Jupyter",
   "lines": 297,
   "truncated": false,
   "block": 6,
   "row": 60
  },
  {
   "path": "notebooks/ASM584v2.ipynb",
   "sha256": "134bdc33dd9b8ea28935321d76036c2f423049b47fdc4210d5388dbf09f73abc",
   "language": "Jupyter",
   "lines": 297,
   "truncated": false,
   "block": 6,
   "row": 65
  },
  {
   "path": "notebooks/BDGP6.ipynb",
   "sha256": "ac42781389cf9173646308959b87239670580b9a4be1fff9dc1cfb3bc482b5d3",
   "language": "Jupyter",
   "lines": 298,
   "truncated": false,
   "block": 6,
   "row": 75
  },
  {
   "path": "notebooks/CriGri_1.0.ipynb",
   "sha256": "a77b2d96af090ac360303cf7941cb69d0a007068a0b985da34e834eeb7f0f10a",
   "language": "Jupyter",
   "lines": 296,
   "truncated": false,
   "block": 6,
   "row": 2
  },
  {
   "path": "notebooks/Epr1.ipynb",
   "sha256": "37ea0138997b5bba8dde8c5f25eee52e22181a53deaca076a5ad9b5525677b21",
   "language": "Jupyter",
   "lines": 298,
   "truncated": false,
   "block": 6,
   "row": 70
  },
  {
   "path": "notebooks/Felis_catus9.0.ipynb",
   "sha256": "33359228030c9584dfacfcacb0d68928b1a70c240cc7a4348133e60c5b5b07e2",
   "language": "Jupyter",
   "lines": 290,
   "truncated": false,
   "block": 5,
   "row": 17748
  },
  {
   "path": "notebooks/GRCg6.ipynb",
   "sha256": "e1c0a310775897cbcdaf3ca6b2719344d26ea840577942cc6fdc2a01f79113d6",
   "language": "Jupyter",
   "lines": 291,
   "truncated": false,
   "block": 5,
   "row": 17761
  },
  {
   "path": "notebooks/GRCz10.ipynb",
   "sha256": "e3026d4f073fc0fde578d0c1427184b005f323df76b4c596cb045539969c1c6f",
   "language": "Jupyter",
   "lines": 289,
   "truncated": false,
   "block": 5,
   "row": 17749
  },
  {
   "path": "notebooks/GRCz11.ipynb",
   "sha256": "2631d7d573fda3a305b115c7853df4ffc8c3cf66a2531fe3b7a4d9a07e2d438c",
   "language": "Jupyter",
   "lines": 293,
   "truncated": false,
   "block": 5,
   "row": 17766
  },
  {
   "path": "notebooks/JGI_4.2.ipynb",
   "sha256": "a74d24275c2cea4709304c8a46578209621e33dac3bb5a659c386fef4485b279",
   "language": "Jupyter",
   "lines": 298,
   "truncated": false,
   "block": 6,
   "row": 66
  },
  {
   "path": "notebooks/MG1655.ipynb",
   "sha256": "bef8ea5c1f5de9625d2032eb19146e76fc4fb528d8625ac155aa89c5c2b1164c",
   "language": "Jupyter",
   "lines": 268,
   "truncated": false,
   "block": 5,
   "row": 17652
  },
  {
   "path": "notebooks/Mmul8.ipynb",
   "sha256": "911e54696489318cfcf8ea9cb3a50e085cf1e3954d2de5212f256f58d699e685",
   "language": "Jupyter",
   "lines": 433,
   "truncated": false,
   "block": 6,
   "row": 401
  },
  {
   "path": "notebooks/PlotCDSSize.ipynb",
   "sha256": "788862c482d0b123f40383c7b504cd9bac9d10f6bde224631312b942efa406b5",
   "language": "Jupyter",
   "lines": 53,
   "truncated": false,
   "block": 5,
   "row": 16260
  },
  {
   "path": "notebooks/R64-1-1-get_UTRs.ipynb",
   "sha256": "231b3c06a518828ce23d74b9f8b3cc01ff8a065545df651a83165e20de980f3a",
   "language": "Jupyter",
   "lines": 126,
   "truncated": false,
   "block": 5,
   "row": 16869
  },
  {
   "path": "notebooks/R64.ipynb",
   "sha256": "d30fed09d409175831aa347a90e49cae705e965c7b2c1e1ddcc5e1ce7df98415",
   "language": "Jupyter",
   "lines": 298,
   "truncated": false,
   "block": 6,
   "row": 76
  },
  {
   "path": "notebooks/Rnor6.0.ipynb",
   "sha256": "0b79f9a3e8a96273b6b8689e3660e94189deb334f44f227b3bc902d9f2c7303d",
   "language": "Jupyter",
   "lines": 296,
   "truncated": false,
   "block": 5,
   "row": 17764
  },
  {
   "path": "notebooks/S_cerevisiae-BY4741-stanford.ipynb",
   "sha256": "e1b25680a0fefc734a6e88a2439573c76ef3eb73be383cf9a1e0efd405753769",
   "language": "Jupyter",
   "lines": 48,
   "truncated": false,
   "block": 5,
   "row": 16275
  },
  {
   "path": "notebooks/TAIR10.ipynb",
   "sha256": "b918c65a94b93ce098fb2096dbe1072fa39b1db6069b4183371ef57f46647056",
   "language": "Jupyter",
   "lines": 298,
   "truncated": false,
   "block": 6,
   "row": 72
  },
  {
   "path": "notebooks/TryBru_Apr2005_chr11.ipynb",
   "sha256": "693e7533dd57a2779e0cd55bcdbe04e0622306a037e2e26efa9d555393760267",
   "language": "Jupyter",
   "lines": 301,
   "truncated": false,
   "block": 5,
   "row": 17760
  },
  {
   "path": "notebooks/WBcel235.ipynb",
   "sha256": "349a68e48b50cade00b2a22e6e06499624f20068712ef3c69c1f087bd0b7e211",
   "language": "Jupyter",
   "lines": 291,
   "truncated": false,
   "block": 5,
   "row": 17765
  },
  {
   "path": "notebooks/archive/Gffutils BDGP6.ipynb",
   "sha256": "6139ed8caeb744307a57e0394a6d0cc517a948b86ae97faaa9802de904abb8ee",
   "language": "Jupyter",
   "lines": 272,
   "truncated": false,
   "block": 5,
   "row": 17723
  },
  {
   "path": "notebooks/archive/Gffutils C_albicans-A22-r50.ipynb",
   "sha256": "54f5d105df027fb37eb632ba49352610441ec1ddbacae83262843cc14792451f",
   "language": "Jupyter",
   "lines": 317,
   "truncated": false,
   "block": 6,
   "row": 154
  },
  {
   "path": "notebooks/archive/Gffutils C_elegans.ipynb",
   "sha256": "2544d5f00d2a0efff0c3490e8b8cfb0a3324028faf047fac6b6d615b5b194dd1",
   "language": "Jupyter",
   "lines": 323,
   "truncated": false,
   "block": 6,
   "row": 169
  },
  {
   "path": "notebooks/archive/Gffutils EColiK12-MG1655.ipynb",
   "sha256": "99b2515149c21b8607bcd4fbbab61b28f5d2433b917073c584d0860f5c40a115",
   "language": "Jupyter",
   "lines": 186,
   "truncated": false,
   "block": 5,
   "row": 17231
  },
  {
   "path": "notebooks/archive/Gffutils Ecoli-B_subtilis.ipynb",
   "sha256": "995fc890925987d86a53b09f38c13a1e885da387baa0d64ff04c0b9312c2c3d2",
   "language": "Jupyter",
   "lines": 275,
   "truncated": false,
   "block": 5,
   "row": 17744
  },
  {
   "path": "notebooks/archive/Gffutils Ecoli-bw25113.ipynb",
   "sha256": "31ca1bf7fd2f75a0d2e0973b3c0ae9e45c4724a3bd9dd5d6c53aa6dd67988db7",
   "language": "Jupyter",
   "lines": 275,
   "truncated": false,
   "block": 5,
   "row": 17742
  },
  {
   "path": "notebooks/archive/Gffutils Ecoli.ipynb",
   "sha256": "71268607c57ebaf5aeaea53385174c26fae120a2debdd5a6f999b7457fa6e543",
   "language": "Jupyter",
   "lines": 276,
   "truncated": false,
   "block": 5,
   "row": 17746
  },
  {
   "path": "notebooks/archive/Gffutils GRCz10.ipynb",
   "sha256": "164f0fe3ca653be5e2a9e5b42553876e6be902097c9a81358d56394f41b5596d",
   "language": "Jupyter",
   "lines": 327,
   "truncated": false,
   "block": 6,
   "row": 177
  },
  {
   "path": "notebooks/archive/Gffutils Human-hg19.ipynb",
   "sha256": "9ec77286c3e5677691fad6a88a0c535ec3be984803b25ac4b474c133ba0899fa",
   "language": "Jupyter",
   "lines": 320,
   "truncated": false,
   "block": 6,
   "row": 138
  },
  {
   "path": "notebooks/archive/Gffutils Human.ipynb",
   "sha256": "a2f264a81088bb71aeeec2c9b2ae7cc3063f7d1ab6cb1c0a12e7e3e13dada9a6",
   "language": "Jupyter",
   "lines": 461,
   "truncated": false,
   "block": 6,
   "row": 630
  },
  {
   "path": "notebooks/archive/Gffutils Mouse.ipynb",
   "sha256": "530153b5f51440826395c147a96bf3e7f97e187f909f56b9f19ecdff88eb4eed",
   "language": "Jupyter",
   "lines": 312,
   "truncated": false,
   "block": 6,
   "row": 125
  },
  {
   "path": "notebooks/archive/Gffutils Rat-Rnor6.ipynb",
   "sha256": "23d5dbd8223152b4e7f0ce362b1b0100cb5eb67f177793cc1ba78db3f0268184",
   "language": "Jupyter",
   "lines": 356,
   "truncated": false,
   "block": 6,
   "row": 283
  },
  {
   "path": "notebooks/archive/Gffutils WBcel235.ipynb",
   "sha256": "79ffad6d85709435371277e4d9fee0f97a5857553d469aade624a4a2f18f2b8a",
   "language": "Jupyter",
   "lines": 302,
   "truncated": false,
   "block": 6,
   "row": 86
  },
  {
   "path": "notebooks/archive/Gffutils dmel6.ipynb",
   "sha256": "8c9a8f14efcc245dfc73dd4a031542cd792dbccf520093321e60f40a4796de67",
   "language": "Jupyter",
   "lines": 266,
   "truncated": false,
   "block": 5,
   "row": 17694
  },
  {
   "path": "notebooks/archive/Gffutils gallus-gallus.ipynb",
   "sha256": "d67f0e977d38caf10e1ccb4bf0ee5284f5745ca2b741c68e22e0766474ec4232",
   "language": "Jupyter",
   "lines": 356,
   "truncated": false,
   "block": 6,
   "row": 296
  },
  {
   "path": "notebooks/archive/Gffutils sacCerR64.ipynb",
   "sha256": "1060e065d09678f84b452702322e6cca1006c15a23b9ae1d1756e0dd32679238",
   "language": "Jupyter",
   "lines": 187,
   "truncated": false,
   "block": 5,
   "row": 17196
  },
  {
   "path": "notebooks/archive/Gffutils xenopus_tropicalis.ipynb",
   "sha256": "d6dd1c1720039f22baaff4ef7850b4f6087814ad8a1d9d22c051cb7e5fc2132e",
   "language": "Jupyter",
   "lines": 356,
   "truncated": false,
   "block": 6,
   "row": 299
  },
  {
   "path": "notebooks/archive/Gffutils-C_elegans.ipynb",
   "sha256": "f653effa5e55a8a8ed48482c1dce0ec02426ca3d424dfc03b58a0fa566add3a7",
   "language": "Jupyter",
   "lines": 275,
   "truncated": false,
   "block": 5,
   "row": 17733
  },
  {
   "path": "notebooks/archive/Gffutils-S_cerevisiae-BY4741.ipynb",
   "sha256": "ba803b9128e2d0e588650a86ba5cda35a0f1f99fa09216275219eb3dfa50036a",
   "language": "Jupyter",
   "lines": 213,
   "truncated": false,
   "block": 5,
   "row": 17416
  },
  {
   "path": "notebooks/archive/Gffutils-S_cerevisiae.ipynb",
   "sha256": "f653effa5e55a8a8ed48482c1dce0ec02426ca3d424dfc03b58a0fa566add3a7",
   "language": "Jupyter",
   "lines": 275,
   "truncated": false,
   "block": 5,
   "row": 17733
  },
  {
   "path": "notebooks/hg38-v96.ipynb",
   "sha256": "5776b1c86c562d0a353891bd9b638883d7944d26a19042a8763e90917bdd5a73",
   "language": "Jupyter",
   "lines": 315,
   "truncated": false,
   "block": 6,
   "row": 38
  },
  {
   "path": "notebooks/hg38.ipynb",
   "sha256": "5e92ed321b75d7c5cb4ff87e45452d21b8396cfce601156f2a4f57706ddcc21a",
   "language": "Jupyter",
   "lines": 293,
   "truncated": false,
   "block": 5,
   "row": 17745
  },
  {
   "path": "notebooks/mm10.ipynb",
   "sha256": "58b74f0d98aa8b5524f059519ced2a187f5efbd7991ae1d5a8e6952eaf382320",
   "language": "Jupyter",
   "lines": 302,
   "truncated": false,
   "block": 6,
   "row": 42
  },
  {
   "path": "notebooks/panTro3.ipynb",
   "sha256": "7d51f1e5adc5700d2c1a983826ab77542e4340cf97560edc6f7cce09f04cd89e",
   "language": "Jupyter",
   "lines": 466,
   "truncated": false,
   "block": 6,
   "row": 464
  },
  {
   "path": "notebooks/rheMac8.ipynb",
   "sha256": "1e12def1f1b182a6b3739d552d4a13cf61edc617c9032e84274e08e0500e32b1",
   "language": "Jupyter",
   "lines": 291,
   "truncated": false,
   "block": 5,
   "row": 17763
  },
  {
   "path": "notebooks/rn6.ipynb",
   "sha256": "f62a892ddba585fee3bb056294b6457a94a9e28f2216e9238f6ef858a6cedb10",
   "language": "Jupyter",
   "lines": 296,
   "truncated": false,
   "block": 5,
   "row": 17762
  },
  {
   "path": "notebooks/sacCerR64.ipynb",
   "sha256": "d1e15acfbe95e68179dee23f156e04123b0f81a0f9b10d5b5df63ec59de470a9",
   "language": "Jupyter",
   "lines": 274,
   "truncated": false,
   "block": 5,
   "row": 17653
  },
  {
   "path": "plot_size_distribution.py",
   "sha256": "0b0fc067abb266192ee545eb495935d3413355d27df87db1e1cdf18a99785e6d",
   "language": "Python",
   "lines": 79,
   "truncated": false,
   "block": 6,
   "row": 34301
  }
 ]
}