{
 "format": "oscr-script-manifest/1",
 "repository": "github.com/goliczgenomelab/nemo",
 "url": "https://github.com/GoliczGenomeLab/nemo",
 "host": "github.com",
 "commit": "a2d4894f166c2a7e1fd6c9553de1393d7d37cd41",
 "license": "MIT",
 "license_confirmed_by": "license file LICENSE",
 "redistribution": "yes",
 "files": [
  {
   "path": "LICENSE",
   "sha256": "39c2d8ee53769046415e3658a2ee5e768a7575781f25b85673eeb6edfe952737",
   "language": "License",
   "lines": 21,
   "truncated": false,
   "block": 1,
   "row": 2173
  },
  {
   "path": "README.md",
   "sha256": "cfcc4ddbc5d56d5d46092abf48d6e9845a7bddecf0ca548641c781c50ff6ff88",
   "language": "Text",
   "lines": 13,
   "truncated": false,
   "block": 1,
   "row": 11782
  },
  {
   "path": "model_configs/nemo/get_full_param_set.sh",
   "sha256": "1e96e878a9f25653670c58016a312fd3a4189a9f622561d768aced654b6e8eec",
   "language": "Shell",
   "lines": 3,
   "truncated": false,
   "block": 1,
   "row": 11122
  },
  {
   "path": "plots/fig_1.R",
   "sha256": "c844fc282635049445aac9cee77a52b0d083bf715a46c14e82a853fc4b5af79e",
   "language": "R",
   "lines": 322,
   "truncated": false,
   "block": 1,
   "row": 10502
  },
  {
   "path": "plots/fig_2.R",
   "sha256": "7d9369a49574854b45e84af336f72502596e30ca6290868264b2e5b40bd38b34",
   "language": "R",
   "lines": 297,
   "truncated": false,
   "block": 1,
   "row": 10445
  },
  {
   "path": "plots/fig_3.R",
   "sha256": "d0d5e98f82c20bd3a8c04584f8474ad55894837bb2e99a58c285ce46e9b06db7",
   "language": "R",
   "lines": 187,
   "truncated": false,
   "block": 1,
   "row": 10349
  },
  {
   "path": "plots/fig_4.R",
   "sha256": "3e27b04f57fb4ea34618f0b7ed9085905627f52770c17c5afbc726ff5111631e",
   "language": "R",
   "lines": 302,
   "truncated": false,
   "block": 1,
   "row": 10441
  },
  {
   "path": "plots/fig_5.R",
   "sha256": "7eeab6227a4ec262da4ac336c93858827597438a7463954f97149537e3a60b16",
   "language": "R",
   "lines": 451,
   "truncated": false,
   "block": 1,
   "row": 10514
  },
  {
   "path": "plots/fig_S10.R",
   "sha256": "5c121b72d0353a9274dde6f11f61088877243f58db841436010b55fdd28a424a",
   "language": "R",
   "lines": 137,
   "truncated": false,
   "block": 1,
   "row": 10269
  },
  {
   "path": "plots/fig_S11-S40.R",
   "sha256": "85bd8433d22f681d4b8cdd2def7def33b0e1f2e20d9694a4e3900afad79c6fe1",
   "language": "R",
   "lines": 195,
   "truncated": false,
   "block": 1,
   "row": 10337
  },
  {
   "path": "plots/fig_S1_S2.R",
   "sha256": "a0e9ca84557b8a686477d3a815da475d40d13b3344ab2879299691b154bdd61c",
   "language": "R",
   "lines": 143,
   "truncated": false,
   "block": 1,
   "row": 10284
  },
  {
   "path": "plots/fig_S4.R",
   "sha256": "6bfb6c4830ae459ee0a1bb84830e0c24657966196751a8e9f8a676f4524cf5af",
   "language": "R",
   "lines": 127,
   "truncated": false,
   "block": 1,
   "row": 10263
  },
  {
   "path": "plots/fig_S41_S42.R",
   "sha256": "d08bcec2a6e00fe42df87441334206923a83dc6a5accc2e9624363d2a975e74e",
   "language": "R",
   "lines": 420,
   "truncated": false,
   "block": 1,
   "row": 10513
  },
  {
   "path": "plots/fig_S43.R",
   "sha256": "eb840947e4472439618a4d1588a44bdc40926aee5a75dddc63d128ff306a9092",
   "language": "R",
   "lines": 59,
   "truncated": false,
   "block": 1,
   "row": 10120
  },
  {
   "path": "plots/fig_S6_S7_S8.R",
   "sha256": "9511c50d6faf982bd760492772856e84ab085d3905bdaac10db5ae37a3c689c2",
   "language": "R",
   "lines": 168,
   "truncated": false,
   "block": 1,
   "row": 10330
  },
  {
   "path": "plots/fig_S9.R",
   "sha256": "ac5d8f18a8b0ce9dfc3fd261bbb8f472901383fb166465c53c19436157abe334",
   "language": "R",
   "lines": 304,
   "truncated": false,
   "block": 1,
   "row": 10409
  },
  {
   "path": "plots/plot_utils.R",
   "sha256": "0d16eceb9476f4ecc61eeb4a204dda2926a3e8c7c96324970c80f4a09421afe9",
   "language": "R",
   "lines": 191,
   "truncated": false,
   "block": 1,
   "row": 10310
  },
  {
   "path": "plots/prep_fig4.R",
   "sha256": "ba92fc35defa0f85b9a007f77bdfb1ea2eb619f605265d6c2941ada2ca4b3fc5",
   "language": "R",
   "lines": 105,
   "truncated": false,
   "block": 1,
   "row": 10212
  },
  {
   "path": "plots/prep_fig4.sh",
   "sha256": "c7de6592740ca86e45aa3f18871bd4bc3c16cf6d7925d596c6f6cb62279d3086",
   "language": "Shell",
   "lines": 13,
   "truncated": false,
   "block": 1,
   "row": 11398
  },
  {
   "path": "scripts/attribution.sh",
   "sha256": "0da78c5a13183e3fab52f2c02b04cf12a3ba97253999617160ae407f3e48e14b",
   "language": "Shell",
   "lines": 77,
   "truncated": false,
   "block": 1,
   "row": 11704
  },
  {
   "path": "scripts/downsample_data.sh",
   "sha256": "b000e886cca4d583e8b93f863a2e5db66c120f1b63e7d8b79dfc396f73e335f7",
   "language": "Shell",
   "lines": 50,
   "truncated": false,
   "block": 1,
   "row": 11677
  },
  {
   "path": "scripts/eval.sh",
   "sha256": "6c449976ff822abd459f555435079bb34215fee0e40b5eb36f513dde3ac6edad",
   "language": "Shell",
   "lines": 135,
   "truncated": false,
   "block": 1,
   "row": 11734
  },
  {
   "path": "scripts/importance.sh",
   "sha256": "ef260732c03f7da21dc455527aa589dcd7494d97645b81b17ce0c182ab7e224f",
   "language": "Shell",
   "lines": 63,
   "truncated": false,
   "block": 1,
   "row": 11698
  },
  {
   "path": "scripts/motif_insertion_pipeline.sh",
   "sha256": "3d0bbf5bfe334b303a37c47a11bbb299cd10d04452ecabd6288268bc2dcc32a2",
   "language": "Shell",
   "lines": 117,
   "truncated": false,
   "block": 1,
   "row": 11740
  },
  {
   "path": "scripts/nemo/attribution/attribution.py",
   "sha256": "18e04b6b19be1e8fb5cef2edb999f52996b7f66cecf4a97c2376790690fe7fa4",
   "language": "Python",
   "lines": 131,
   "truncated": false,
   "block": 1,
   "row": 7507
  },
  {
   "path": "scripts/nemo/attribution/concat_attribs.py",
   "sha256": "23775c63ba6eb7cbb140e763d5ff9c92eb730a542109974e77f795316b19a3cb",
   "language": "Python",
   "lines": 98,
   "truncated": false,
   "block": 1,
   "row": 7038
  },
  {
   "path": "scripts/nemo/attribution/get_full_importance.py",
   "sha256": "825870bc0c70ef917f1597cf995692b10aab711128b6f0ac2fd6f8b230b753e6",
   "language": "Python",
   "lines": 117,
   "truncated": false,
   "block": 1,
   "row": 7397
  },
  {
   "path": "scripts/nemo/attribution/get_trimmed_importance.py",
   "sha256": "814a5aaa0caaefcb49c51f9e2729c5e5ad6c1faf48e639cb79ebd19cd8a00841",
   "language": "Python",
   "lines": 109,
   "truncated": false,
   "block": 1,
   "row": 7360
  },
  {
   "path": "scripts/nemo/eval/cat_preds.sh",
   "sha256": "c0f52efe029e93bb81cc8b18df42a7a49d14bf178e4a6841f92bcdbc2b19c5f3",
   "language": "Shell",
   "lines": 56,
   "truncated": false,
   "block": 1,
   "row": 11689
  },
  {
   "path": "scripts/nemo/eval/eval.py",
   "sha256": "e79f5e560cda401a94006df85fa18626d7e2ca375782682ef02589b80327531c",
   "language": "Python",
   "lines": 312,
   "truncated": false,
   "block": 1,
   "row": 8719
  },
  {
   "path": "scripts/nemo/eval/get_expression_class_lists.R",
   "sha256": "16f55977be327bbae07dceb8b0e1ca9930538426b5415a25263963f6d066ed31",
   "language": "R",
   "lines": 73,
   "truncated": false,
   "block": 1,
   "row": 10160
  },
  {
   "path": "scripts/nemo/eval/get_rsq_matrix.R",
   "sha256": "e3056a6a50871fbaf16d210e887cb230fe866621e12d91ea26ad79912a8985df",
   "language": "R",
   "lines": 163,
   "truncated": false,
   "block": 1,
   "row": 10338
  },
  {
   "path": "scripts/nemo/eval/over_under_pred.R",
   "sha256": "3e162ce2929f018fdecfc3b2bcb3fd03428452203b4e56331e0131dcbef70520",
   "language": "R",
   "lines": 72,
   "truncated": false,
   "block": 1,
   "row": 10150
  },
  {
   "path": "scripts/nemo/hyperparam_tuning/final_touches.py",
   "sha256": "c613a368326b21db210d5c32c7f2f2ca22bd116faa641ccd3e539e89c8771d70",
   "language": "Python",
   "lines": 355,
   "truncated": false,
   "block": 1,
   "row": 8928
  },
  {
   "path": "scripts/nemo/hyperparam_tuning/finetune_architecture.py",
   "sha256": "eedae5180c0ce2d58f1fd4269179694f9e36edaaffc59b90ec6353d960928c6a",
   "language": "Python",
   "lines": 421,
   "truncated": false,
   "block": 1,
   "row": 9118
  },
  {
   "path": "scripts/nemo/hyperparam_tuning/finetune_learning.py",
   "sha256": "aec4710efcc167d358209aa13992a204701015659c9574746b9c7ebe4ea3b799",
   "language": "Python",
   "lines": 340,
   "truncated": false,
   "block": 1,
   "row": 8897
  },
  {
   "path": "scripts/nemo/hyperparam_tuning/get_completed_trials.py",
   "sha256": "56249b6cb27736c77e7943839de24e29f023f01fe75b1793e47c0d3a10df004c",
   "language": "Python",
   "lines": 43,
   "truncated": false,
   "block": 1,
   "row": 6194
  },
  {
   "path": "scripts/nemo/hyperparam_tuning/optimize_architecture.py",
   "sha256": "38b7a118a8a48deba686a9d3790373828ad054ec0877a275a997c096c4534a9d",
   "language": "Python",
   "lines": 503,
   "truncated": false,
   "block": 1,
   "row": 9362
  },
  {
   "path": "scripts/nemo/hyperparam_tuning/optimize_learning.py",
   "sha256": "643cc9d96cf12e8a1316e7bd4277143098715c849f488377ab34abcf8d5ca9fd",
   "language": "Python",
   "lines": 331,
   "truncated": false,
   "block": 1,
   "row": 8878
  },
  {
   "path": "scripts/nemo/hyperparam_tuning/validate_architecture.py",
   "sha256": "2bbd05a40d085a7d81653029afa0c96cef19c4275c3f8426e226a1c09a23cebc",
   "language": "Python",
   "lines": 426,
   "truncated": false,
   "block": 1,
   "row": 9038
  },
  {
   "path": "scripts/nemo/model_stats.py",
   "sha256": "752a641d75a6b368fd3e5f18271dd69ce48a5c76b7050889a02bfd8f2a18307d",
   "language": "Python",
   "lines": 51,
   "truncated": false,
   "block": 1,
   "row": 6261
  },
  {
   "path": "scripts/nemo/mutation/mutate_sequences.py",
   "sha256": "97a407ac864da7bf5c9989c42e90beb4ee22ea8f68e88fc0789e28d9c27e8630",
   "language": "Python",
   "lines": 247,
   "truncated": false,
   "block": 1,
   "row": 8714
  },
  {
   "path": "scripts/nemo/preprocessing/clean_up_expression_matrix.R",
   "sha256": "73dcad901557c0f08d2c04ff0f68f3aae1c019b12e570e9e59e61eb50b0bfaf5",
   "language": "R",
   "lines": 75,
   "truncated": false,
   "block": 1,
   "row": 10149
  },
  {
   "path": "scripts/nemo/preprocessing/csv_to_fasta.py",
   "sha256": "e7cfb0ebb36c752b279f00ba0a36158dccb88dc24a826f7a3a604a145ec57b2f",
   "language": "Python",
   "lines": 97,
   "truncated": false,
   "block": 1,
   "row": 7187
  },
  {
   "path": "scripts/nemo/preprocessing/downsample_data.py",
   "sha256": "8122ef5ba8078bdac803a6983416c5666a92e63fa3aa90b3610e5cd9112e4c71",
   "language": "Python",
   "lines": 60,
   "truncated": false,
   "block": 1,
   "row": 6512
  },
  {
   "path": "scripts/nemo/preprocessing/get_len_gc.py",
   "sha256": "bbecd534f24d3c15ab004b325248605897ea1aa37bd8f873140fc11e3be1fbd3",
   "language": "Python",
   "lines": 98,
   "truncated": false,
   "block": 1,
   "row": 6936
  },
  {
   "path": "scripts/nemo/preprocessing/get_median.R",
   "sha256": "7cc21def3555785be0008e538ff3108b7b41acc566ee213404d854f6b645e882",
   "language": "R",
   "lines": 71,
   "truncated": false,
   "block": 1,
   "row": 10141
  },
  {
   "path": "scripts/nemo/preprocessing/get_promoter_terminator.py",
   "sha256": "71f729f35d4e3a3802ae0c3a5cd53ba60aef1b71d5acb641df6f35a41597370b",
   "language": "Python",
   "lines": 210,
   "truncated": false,
   "block": 1,
   "row": 8532
  },
  {
   "path": "scripts/nemo/preprocessing/get_rep_avrg.R",
   "sha256": "9aa59bf1f36c4176caf100cdc15cf9b0d8967e459912d03b9897075a4f40bd61",
   "language": "R",
   "lines": 67,
   "truncated": false,
   "block": 1,
   "row": 10142
  },
  {
   "path": "scripts/nemo/preprocessing/gff2bed.py",
   "sha256": "551cbc938e8c1e64089a73c52145e438e531724bb5ad241b43a056cece72b43e",
   "language": "Python",
   "lines": 47,
   "truncated": false,
   "block": 1,
   "row": 6287
  },
  {
   "path": "scripts/nemo/preprocessing/graphpart_prep_only_expressed.R",
   "sha256": "3e946e35789431685e3441724f51a16d4ca4a0e23f7cf527ea0bc697c91bfbe9",
   "language": "R",
   "lines": 106,
   "truncated": false,
   "block": 1,
   "row": 10261
  },
  {
   "path": "scripts/nemo/preprocessing/merge_data.py",
   "sha256": "3c4ef15046cb91abad90d435b9c8fee5abd9489e4ce5ec2320e81d6cacb8aa7a",
   "language": "Python",
   "lines": 304,
   "truncated": false,
   "block": 1,
   "row": 8590
  },
  {
   "path": "scripts/nemo/preprocessing/multiline_to_singleline_fasta.sh",
   "sha256": "cc7d60c24de302ab19da435ac84e6e79b1e6c87a6280230217a20d6f7cd23f6a",
   "language": "Shell",
   "lines": 44,
   "truncated": false,
   "block": 1,
   "row": 11671
  },
  {
   "path": "scripts/nemo/preprocessing/remove_low_corr_samples.R",
   "sha256": "41ca403ac28e85827c3c9fd70c5765e33e9d82bd175f59224f7f94371866d4e7",
   "language": "R",
   "lines": 92,
   "truncated": false,
   "block": 1,
   "row": 10163
  },
  {
   "path": "scripts/nemo/preprocessing/setup_folds.py",
   "sha256": "6dc7c67ada511bdd7c39a0b663b91801be04df17834041f3f020ded697c00fd8",
   "language": "Python",
   "lines": 234,
   "truncated": false,
   "block": 1,
   "row": 8517
  },
  {
   "path": "scripts/nemo/preprocessing/setup_full.py",
   "sha256": "37179634a572588a46a7fec5aa440d4a78e56cc7202cbe595895b1b6ffd3bb09",
   "language": "Python",
   "lines": 118,
   "truncated": false,
   "block": 1,
   "row": 7203
  },
  {
   "path": "scripts/nemo/preprocessing/shuffle_graphpart_clusters.py",
   "sha256": "afbd8d0c1b5684733838cf312b39700ef23b90a757d735e3ae9f8be18536e55d",
   "language": "Python",
   "lines": 49,
   "truncated": false,
   "block": 1,
   "row": 6342
  },
  {
   "path": "scripts/nemo/run_training.py",
   "sha256": "314aad2778335f42c7c2df029f89682556492a335ec64f24b36670f98f788360",
   "language": "Python",
   "lines": 430,
   "truncated": false,
   "block": 1,
   "row": 9106
  },
  {
   "path": "scripts/nemo/utils/attrib_utils.py",
   "sha256": "a25a733da12e30bb48ab4693cd69e46598fbbb03b657ad1238564b206fa695a4",
   "language": "Python",
   "lines": 279,
   "truncated": false,
   "block": 1,
   "row": 8841
  },
  {
   "path": "scripts/nemo/utils/eval_utils.R",
   "sha256": "fb98b30955067257f417da3a3c03456272c4561155d68bcd235978902fb50d5c",
   "language": "R",
   "lines": 90,
   "truncated": false,
   "block": 1,
   "row": 10168
  },
  {
   "path": "scripts/nemo/utils/model_utils.py",
   "sha256": "fe893961c963532939f030f58a92a7bd719dfeeced91831095468026cfc14f7c",
   "language": "Python",
   "lines": 678,
   "truncated": false,
   "block": 1,
   "row": 9538
  },
  {
   "path": "scripts/prep_Athaliana.sh",
   "sha256": "be867226f8840d46e9ce40011ef3441ae86ae06972e55a4de96adb6400a3d327",
   "language": "Shell",
   "lines": 163,
   "truncated": false,
   "block": 1,
   "row": 11741
  },
  {
   "path": "scripts/prep_Bnapus.sh",
   "sha256": "eb64bc4fd3f243e0337f706b51e49f9066fb2b153eb3ee2383d140c0f378094e",
   "language": "Shell",
   "lines": 174,
   "truncated": false,
   "block": 1,
   "row": 11743
  },
  {
   "path": "scripts/run_setup.sh",
   "sha256": "c8ab43614e647ab973b2bf1db1855dacbfec9695de1ce2f1f928b4f0ff4636ca",
   "language": "Shell",
   "lines": 101,
   "truncated": false,
   "block": 1,
   "row": 11718
  },
  {
   "path": "scripts/setup_files.sh",
   "sha256": "50ca22e7b9a325d15ea385c9271278199c61c4b8d9e09eb9b959799c2e372bd2",
   "language": "Shell",
   "lines": 221,
   "truncated": false,
   "block": 1,
   "row": 11746
  },
  {
   "path": "scripts/train.sh",
   "sha256": "16b87f2f2e7390a52784bd66307dbc7963bda775ef00f86a9e9172297def4820",
   "language": "Shell",
   "lines": 77,
   "truncated": false,
   "block": 1,
   "row": 11700
  },
  {
   "path": "scripts/train_Athaliana.sh",
   "sha256": "194fce5c201ff7f6418bb49600b4c4f92a458271462e85370776115c131fd14b",
   "language": "Shell",
   "lines": 56,
   "truncated": false,
   "block": 1,
   "row": 11673
  },
  {
   "path": "scripts/train_Bnapus.sh",
   "sha256": "258b2892b0c0626be66612e597ebb9b4ca7cf29fbdb68c8c1025468755648047",
   "language": "Shell",
   "lines": 80,
   "truncated": false,
   "block": 1,
   "row": 11701
  },
  {
   "path": "scripts/tune_hyperparams.sh",
   "sha256": "98173bee60b4e18729af9282ed7f82faa40e07878471294bc54554819bc4a071",
   "language": "Shell",
   "lines": 96,
   "truncated": false,
   "block": 1,
   "row": 11722
  }
 ]
}