{
 "format": "oscr-script-manifest/1",
 "repository": "github.com/wangjr03/flamingo",
 "url": "https://github.com/wangjr03/FLAMINGO",
 "host": "github.com",
 "commit": "b81cde591bcea2cdced5bd60ade0088927806e22",
 "license": "MIT",
 "license_confirmed_by": "license file LICENSE",
 "redistribution": "yes",
 "files": [
  {
   "path": "FLAMINGOr/R/flamingo.assemble_structure.R",
   "sha256": "9b6757273185867b5367c3e7316220ad36f048e21d9a0f04d4c4902b1b22d506",
   "language": "R",
   "lines": 148,
   "truncated": false,
   "block": 23,
   "row": 16174
  },
  {
   "path": "FLAMINGOr/R/flamingo.calculating_epigenomic_signal.R",
   "sha256": "4bfea8cc7af0effbf1d0df1c3472d54a35958d04799fa37cde546ee3902e8f88",
   "language": "R",
   "lines": 22,
   "truncated": false,
   "block": 23,
   "row": 15592
  },
  {
   "path": "FLAMINGOr/R/flamingo.construct_flamingo_from_hic.R",
   "sha256": "fc89819c18fb68b9c74361d47c1374616462c043259ab7b2ad586085700e6ce5",
   "language": "R",
   "lines": 33,
   "truncated": false,
   "block": 23,
   "row": 15641
  },
  {
   "path": "FLAMINGOr/R/flamingo.construct_flamingo_from_mcool.R",
   "sha256": "6a246274ba9e0d8e36086eb45569533af41df39128a3907b378ddb0f284d6940",
   "language": "R",
   "lines": 52,
   "truncated": false,
   "block": 23,
   "row": 15806
  },
  {
   "path": "FLAMINGOr/R/flamingo.construct_flamingo_from_sparse_matrix.R",
   "sha256": "8500c516030a551643de44901cc9b199e4c0878f27b0c625f12dbde4b894f7f4",
   "language": "R",
   "lines": 41,
   "truncated": false,
   "block": 23,
   "row": 15686
  },
  {
   "path": "FLAMINGOr/R/flamingo.divide_domain.R",
   "sha256": "f3370b3bafb7e546cbfd8fe1be725c2ca506a4b1afb660f126b419fabc2e17f2",
   "language": "R",
   "lines": 41,
   "truncated": false,
   "block": 23,
   "row": 15691
  },
  {
   "path": "FLAMINGOr/R/flamingo.estimate_alpha.R",
   "sha256": "1d8d7ae537100c03e3216a71b0c069945d4ba6f39c452b62b30f69963af3b6af",
   "language": "R",
   "lines": 14,
   "truncated": false,
   "block": 23,
   "row": 15483
  },
  {
   "path": "FLAMINGOr/R/flamingo.impute_dist_from_epi.R",
   "sha256": "df6bd29940d17910210b0fa7570d7274af9b6bf0171b9e8b47c8003dd9209534",
   "language": "R",
   "lines": 26,
   "truncated": false,
   "block": 23,
   "row": 15588
  },
  {
   "path": "FLAMINGOr/R/flamingo.init_object.R",
   "sha256": "97eeaac83e59e9a3448e3629a49511c7959d955e052e4c5b187e2db1d643c693",
   "language": "R",
   "lines": 9,
   "truncated": false,
   "block": 23,
   "row": 15501
  },
  {
   "path": "FLAMINGOr/R/flamingo.main_func.R",
   "sha256": "6a1c2c333bbdf83d3a570d6165d84fd878196e1088318cceb937633c5ece16cb",
   "language": "R",
   "lines": 89,
   "truncated": false,
   "block": 23,
   "row": 16285
  },
  {
   "path": "FLAMINGOr/R/flamingo.main_func_large.R",
   "sha256": "7ac6b5ed098e004684c152bed5e7290c152d2a35afe3f86815a7c98ae928a031",
   "language": "R",
   "lines": 106,
   "truncated": false,
   "block": 23,
   "row": 16383
  },
  {
   "path": "FLAMINGOr/R/flamingo.reconstruct_backbone_structure.R",
   "sha256": "9a1612155a730aa4cd2d6230d14f1a8f6feb5024607f4856087c6281542a4ca8",
   "language": "R",
   "lines": 15,
   "truncated": false,
   "block": 23,
   "row": 15558
  },
  {
   "path": "FLAMINGOr/R/flamingo.reconstruct_structure.R",
   "sha256": "dc6319a88aadba8e8b7f99cc5ebbb1db67a4f082fb9f782c3eef296c046eedf0",
   "language": "R",
   "lines": 32,
   "truncated": false,
   "block": 23,
   "row": 15615
  },
  {
   "path": "FLAMINGOr/R/flamingo.reconstruct_structure_worker.R",
   "sha256": "bd6854334dd519a4fc482b51b72056dc1121cfc56825be0463faed8f5384b0d4",
   "language": "R",
   "lines": 99,
   "truncated": false,
   "block": 23,
   "row": 15996
  },
  {
   "path": "FLAMINGOr/R/flamingo.reconstruct_structure_wraper.R",
   "sha256": "541a7d16a39f672e72f68209b3ecc337376e3410c017b9a0f84f57fdb09cf72b",
   "language": "R",
   "lines": 23,
   "truncated": false,
   "block": 23,
   "row": 15565
  },
  {
   "path": "FLAMINGOr/R/flamingo.utils.R",
   "sha256": "e30fde02dfe5f055d4f576565c2c20758b4488a5c77eca00df70a6909640111d",
   "language": "R",
   "lines": 321,
   "truncated": false,
   "block": 23,
   "row": 16378
  },
  {
   "path": "FLAMINGOr/R/iflamingo.main_func.R",
   "sha256": "4deaff726cecfc907d2051c2fbf738cf12e0148fdd5729c4f6b82001dc12a9a4",
   "language": "R",
   "lines": 94,
   "truncated": false,
   "block": 23,
   "row": 16309
  },
  {
   "path": "FLAMINGOr/R/iflamingo.reconstruct_structure.R",
   "sha256": "28c9f168e4e5421269e0295b6c88901df014d7fc036487d407300386c65c7e77",
   "language": "R",
   "lines": 32,
   "truncated": false,
   "block": 23,
   "row": 15627
  },
  {
   "path": "FLAMINGOr/R/iflamingo.reconstruct_structure_worker.R",
   "sha256": "4d3a9afca2f07ed10ff5abed36552a3da7d3e1a7314ace7139ccd2a4f56fe014",
   "language": "R",
   "lines": 98,
   "truncated": false,
   "block": 23,
   "row": 16016
  },
  {
   "path": "FLAMINGOr/R/iflamingo.reconstruct_structure_wraper.R",
   "sha256": "4335e941f03fcc46e33d606452f4f4993de874733abd5c2afb2fa943908d6447",
   "language": "R",
   "lines": 25,
   "truncated": false,
   "block": 23,
   "row": 15605
  },
  {
   "path": "FLAMINGOr/R/write.vtk.R",
   "sha256": "e56d576beae24d081d54f786b37881080d0a25a0f45bab749999bbb40e636376",
   "language": "R",
   "lines": 28,
   "truncated": false,
   "block": 23,
   "row": 15706
  },
  {
   "path": "FLAMINGOr/tests/testthat.R",
   "sha256": "45da4de9747181f3f04aa72dc51d8736a5a735ed4a08abc6c3e6172643059104",
   "language": "R",
   "lines": 4,
   "truncated": false,
   "block": 23,
   "row": 15419
  },
  {
   "path": "FLAMINGOr/tests/testthat/test-flamingo.R",
   "sha256": "79b0200c9538c47e4aa5a7a3404d653c1f468e25be95bc042724bd7d2e558b34",
   "language": "R",
   "lines": 3,
   "truncated": false,
   "block": 23,
   "row": 15422
  },
  {
   "path": "LICENSE",
   "sha256": "179ae4b080d68285de47b679449cb91fbbbcdf33aaac0b42bb3d3f9fbf8d854f",
   "language": "License",
   "lines": 21,
   "truncated": false,
   "block": 22,
   "row": 13882
  },
  {
   "path": "README.md",
   "sha256": "01ffa11080ca0922830c9f40329686ab329d53e2adcfa36459d246b926b25101",
   "language": "Text",
   "lines": 300,
   "truncated": false,
   "block": 24,
   "row": 968
  },
  {
   "path": "code/1_preprocess_HiC.R",
   "sha256": "69f4d4634df6fdb9258c78e8caecf942a0b20df9bfd02bc5532e4dce1d1046f9",
   "language": "R",
   "lines": 49,
   "truncated": false,
   "block": 23,
   "row": 15576
  },
  {
   "path": "code/2_generate_fragment_data.R",
   "sha256": "1d1d57f72d256e195688c63ae2314415620dbe229b19341dfb06bad9902501d1",
   "language": "R",
   "lines": 26,
   "truncated": false,
   "block": 23,
   "row": 15524
  },
  {
   "path": "code/3_generate_fragment_DNase.R",
   "sha256": "4866f1a5e044d08e0a5e59a7476b3d783e0389542ad97edba8886f83637ddaf1",
   "language": "R",
   "lines": 21,
   "truncated": false,
   "block": 23,
   "row": 15498
  },
  {
   "path": "code/4_generate_DNase_profile.R",
   "sha256": "80fcc22bce90b585689e00b90660bd3ac85be7f8c91042f6a6cfb0c70757d6ad",
   "language": "R",
   "lines": 34,
   "truncated": false,
   "block": 23,
   "row": 15545
  },
  {
   "path": "code/4_generate_DNase_profile.sh",
   "sha256": "156131284bcdc106827255966c9f79923818c616d7c82adfd1a434bd33a2d4c3",
   "language": "Shell",
   "lines": 8,
   "truncated": false,
   "block": 23,
   "row": 17122
  },
  {
   "path": "code/5_impute_DNase_dist.R",
   "sha256": "ddf3dd0df78a2a3cb4252e8db662d5bee8cc1817b0a3c0811bc7a14d3ce48b6d",
   "language": "R",
   "lines": 30,
   "truncated": false,
   "block": 23,
   "row": 15556
  },
  {
   "path": "code/6_generate_backbone_data.R",
   "sha256": "d62c6e72f481b25b959cbf1b116eae971d754abbce82e9fc3115e52fc73d8582",
   "language": "R",
   "lines": 43,
   "truncated": false,
   "block": 23,
   "row": 15569
  },
  {
   "path": "code/7_reconstruct_model_DNase.R",
   "sha256": "d7c282cf7d1e159022637fd58d67cbafeb1845b730589159b254c7f4522b45dc",
   "language": "R",
   "lines": 366,
   "truncated": false,
   "block": 23,
   "row": 16325
  },
  {
   "path": "code/7_reconstruct_within_cellline.R",
   "sha256": "810ca8e902b80cc4d915837de3630118c87dbb13aedd49d877c65b4997ac0354",
   "language": "R",
   "lines": 354,
   "truncated": false,
   "block": 23,
   "row": 16283
  },
  {
   "path": "code/8_ensemble_structure_V2.R",
   "sha256": "accaffacc9d60de5fab7b34cfab0aadec0504301c80f7ef37fe3340073d4bc14",
   "language": "R",
   "lines": 244,
   "truncated": false,
   "block": 23,
   "row": 16239
  },
  {
   "path": "code/process_data_wrapper.sh",
   "sha256": "f634ccc361b90a030901b875b5b2b93b817a6a3cb7fb08636430c54fac3ba1c9",
   "language": "Shell",
   "lines": 7,
   "truncated": false,
   "block": 23,
   "row": 17269
  }
 ]
}