Team Ai
Datasetpublic

OpenScientificCodeRegistry/Database

Open Scientific Code Registry (OSCR): the authors' scripts The code published by the authors of open-access neuroscience papers, as found and verified by Open Scientific Code Registry (OSCR). Each file is here exactly as it is at the source, at the verified commit, under the license of its repository. 421,275 unique files (3,782 MB of text) from 8,849 repositories, in 24 Parquet block(s). Only files whose repository's license allows redistribution, confirmed by the repository's… See the full description on the dataset page: https://huggingface.co/datasets/OpenScientificCodeRegistry/Database.

sourceHugging Faceotherupdated 2d agoView on Hugging Face
0likes5.6kdownloads
github.com__goliczgenomelab__nemo.json633 linesDownload Raw Back to 23
1{2 "format": "oscr-script-manifest/1",3 "repository": "github.com/goliczgenomelab/nemo",4 "url": "https://github.com/GoliczGenomeLab/nemo",5 "host": "github.com",6 "commit": "a2d4894f166c2a7e1fd6c9553de1393d7d37cd41",7 "license": "MIT",8 "license_confirmed_by": "license file LICENSE",9 "redistribution": "yes",10 "files": [11  {12   "path": "LICENSE",13   "sha256": "39c2d8ee53769046415e3658a2ee5e768a7575781f25b85673eeb6edfe952737",14   "language": "License",15   "lines": 21,16   "truncated": false,17   "block": 1,18   "row": 217319  },20  {21   "path": "README.md",22   "sha256": "cfcc4ddbc5d56d5d46092abf48d6e9845a7bddecf0ca548641c781c50ff6ff88",23   "language": "Text",24   "lines": 13,25   "truncated": false,26   "block": 1,27   "row": 1178228  },29  {30   "path": "model_configs/nemo/get_full_param_set.sh",31   "sha256": "1e96e878a9f25653670c58016a312fd3a4189a9f622561d768aced654b6e8eec",32   "language": "Shell",33   "lines": 3,34   "truncated": false,35   "block": 1,36   "row": 1112237  },38  {39   "path": "plots/fig_1.R",40   "sha256": "c844fc282635049445aac9cee77a52b0d083bf715a46c14e82a853fc4b5af79e",41   "language": "R",42   "lines": 322,43   "truncated": false,44   "block": 1,45   "row": 1050246  },47  {48   "path": "plots/fig_2.R",49   "sha256": "7d9369a49574854b45e84af336f72502596e30ca6290868264b2e5b40bd38b34",50   "language": "R",51   "lines": 297,52   "truncated": false,53   "block": 1,54   "row": 1044555  },56  {57   "path": "plots/fig_3.R",58   "sha256": "d0d5e98f82c20bd3a8c04584f8474ad55894837bb2e99a58c285ce46e9b06db7",59   "language": "R",60   "lines": 187,61   "truncated": false,62   "block": 1,63   "row": 1034964  },65  {66   "path": "plots/fig_4.R",67   "sha256": "3e27b04f57fb4ea34618f0b7ed9085905627f52770c17c5afbc726ff5111631e",68   "language": "R",69   "lines": 302,70   "truncated": false,71   "block": 1,72   "row": 1044173  },74  {75   "path": "plots/fig_5.R",76   "sha256": "7eeab6227a4ec262da4ac336c93858827597438a7463954f97149537e3a60b16",77   "language": "R",78   "lines": 451,79   "truncated": false,80   "block": 1,81   "row": 1051482  },83  {84   "path": "plots/fig_S10.R",85   "sha256": "5c121b72d0353a9274dde6f11f61088877243f58db841436010b55fdd28a424a",86   "language": "R",87   "lines": 137,88   "truncated": false,89   "block": 1,90   "row": 1026991  },92  {93   "path": "plots/fig_S11-S40.R",94   "sha256": "85bd8433d22f681d4b8cdd2def7def33b0e1f2e20d9694a4e3900afad79c6fe1",95   "language": "R",96   "lines": 195,97   "truncated": false,98   "block": 1,99   "row": 10337100  },101  {102   "path": "plots/fig_S1_S2.R",103   "sha256": "a0e9ca84557b8a686477d3a815da475d40d13b3344ab2879299691b154bdd61c",104   "language": "R",105   "lines": 143,106   "truncated": false,107   "block": 1,108   "row": 10284109  },110  {111   "path": "plots/fig_S4.R",112   "sha256": "6bfb6c4830ae459ee0a1bb84830e0c24657966196751a8e9f8a676f4524cf5af",113   "language": "R",114   "lines": 127,115   "truncated": false,116   "block": 1,117   "row": 10263118  },119  {120   "path": "plots/fig_S41_S42.R",121   "sha256": "d08bcec2a6e00fe42df87441334206923a83dc6a5accc2e9624363d2a975e74e",122   "language": "R",123   "lines": 420,124   "truncated": false,125   "block": 1,126   "row": 10513127  },128  {129   "path": "plots/fig_S43.R",130   "sha256": "eb840947e4472439618a4d1588a44bdc40926aee5a75dddc63d128ff306a9092",131   "language": "R",132   "lines": 59,133   "truncated": false,134   "block": 1,135   "row": 10120136  },137  {138   "path": "plots/fig_S6_S7_S8.R",139   "sha256": "9511c50d6faf982bd760492772856e84ab085d3905bdaac10db5ae37a3c689c2",140   "language": "R",141   "lines": 168,142   "truncated": false,143   "block": 1,144   "row": 10330145  },146  {147   "path": "plots/fig_S9.R",148   "sha256": "ac5d8f18a8b0ce9dfc3fd261bbb8f472901383fb166465c53c19436157abe334",149   "language": "R",150   "lines": 304,151   "truncated": false,152   "block": 1,153   "row": 10409154  },155  {156   "path": "plots/plot_utils.R",157   "sha256": "0d16eceb9476f4ecc61eeb4a204dda2926a3e8c7c96324970c80f4a09421afe9",158   "language": "R",159   "lines": 191,160   "truncated": false,161   "block": 1,162   "row": 10310163  },164  {165   "path": "plots/prep_fig4.R",166   "sha256": "ba92fc35defa0f85b9a007f77bdfb1ea2eb619f605265d6c2941ada2ca4b3fc5",167   "language": "R",168   "lines": 105,169   "truncated": false,170   "block": 1,171   "row": 10212172  },173  {174   "path": "plots/prep_fig4.sh",175   "sha256": "c7de6592740ca86e45aa3f18871bd4bc3c16cf6d7925d596c6f6cb62279d3086",176   "language": "Shell",177   "lines": 13,178   "truncated": false,179   "block": 1,180   "row": 11398181  },182  {183   "path": "scripts/attribution.sh",184   "sha256": "0da78c5a13183e3fab52f2c02b04cf12a3ba97253999617160ae407f3e48e14b",185   "language": "Shell",186   "lines": 77,187   "truncated": false,188   "block": 1,189   "row": 11704190  },191  {192   "path": "scripts/downsample_data.sh",193   "sha256": "b000e886cca4d583e8b93f863a2e5db66c120f1b63e7d8b79dfc396f73e335f7",194   "language": "Shell",195   "lines": 50,196   "truncated": false,197   "block": 1,198   "row": 11677199  },200  {201   "path": "scripts/eval.sh",202   "sha256": "6c449976ff822abd459f555435079bb34215fee0e40b5eb36f513dde3ac6edad",203   "language": "Shell",204   "lines": 135,205   "truncated": false,206   "block": 1,207   "row": 11734208  },209  {210   "path": "scripts/importance.sh",211   "sha256": "ef260732c03f7da21dc455527aa589dcd7494d97645b81b17ce0c182ab7e224f",212   "language": "Shell",213   "lines": 63,214   "truncated": false,215   "block": 1,216   "row": 11698217  },218  {219   "path": "scripts/motif_insertion_pipeline.sh",220   "sha256": "3d0bbf5bfe334b303a37c47a11bbb299cd10d04452ecabd6288268bc2dcc32a2",221   "language": "Shell",222   "lines": 117,223   "truncated": false,224   "block": 1,225   "row": 11740226  },227  {228   "path": "scripts/nemo/attribution/attribution.py",229   "sha256": "18e04b6b19be1e8fb5cef2edb999f52996b7f66cecf4a97c2376790690fe7fa4",230   "language": "Python",231   "lines": 131,232   "truncated": false,233   "block": 1,234   "row": 7507235  },236  {237   "path": "scripts/nemo/attribution/concat_attribs.py",238   "sha256": "23775c63ba6eb7cbb140e763d5ff9c92eb730a542109974e77f795316b19a3cb",239   "language": "Python",240   "lines": 98,241   "truncated": false,242   "block": 1,243   "row": 7038244  },245  {246   "path": "scripts/nemo/attribution/get_full_importance.py",247   "sha256": "825870bc0c70ef917f1597cf995692b10aab711128b6f0ac2fd6f8b230b753e6",248   "language": "Python",249   "lines": 117,250   "truncated": false,251   "block": 1,252   "row": 7397253  },254  {255   "path": "scripts/nemo/attribution/get_trimmed_importance.py",256   "sha256": "814a5aaa0caaefcb49c51f9e2729c5e5ad6c1faf48e639cb79ebd19cd8a00841",257   "language": "Python",258   "lines": 109,259   "truncated": false,260   "block": 1,261   "row": 7360262  },263  {264   "path": "scripts/nemo/eval/cat_preds.sh",265   "sha256": "c0f52efe029e93bb81cc8b18df42a7a49d14bf178e4a6841f92bcdbc2b19c5f3",266   "language": "Shell",267   "lines": 56,268   "truncated": false,269   "block": 1,270   "row": 11689271  },272  {273   "path": "scripts/nemo/eval/eval.py",274   "sha256": "e79f5e560cda401a94006df85fa18626d7e2ca375782682ef02589b80327531c",275   "language": "Python",276   "lines": 312,277   "truncated": false,278   "block": 1,279   "row": 8719280  },281  {282   "path": "scripts/nemo/eval/get_expression_class_lists.R",283   "sha256": "16f55977be327bbae07dceb8b0e1ca9930538426b5415a25263963f6d066ed31",284   "language": "R",285   "lines": 73,286   "truncated": false,287   "block": 1,288   "row": 10160289  },290  {291   "path": "scripts/nemo/eval/get_rsq_matrix.R",292   "sha256": "e3056a6a50871fbaf16d210e887cb230fe866621e12d91ea26ad79912a8985df",293   "language": "R",294   "lines": 163,295   "truncated": false,296   "block": 1,297   "row": 10338298  },299  {300   "path": "scripts/nemo/eval/over_under_pred.R",301   "sha256": "3e162ce2929f018fdecfc3b2bcb3fd03428452203b4e56331e0131dcbef70520",302   "language": "R",303   "lines": 72,304   "truncated": false,305   "block": 1,306   "row": 10150307  },308  {309   "path": "scripts/nemo/hyperparam_tuning/final_touches.py",310   "sha256": "c613a368326b21db210d5c32c7f2f2ca22bd116faa641ccd3e539e89c8771d70",311   "language": "Python",312   "lines": 355,313   "truncated": false,314   "block": 1,315   "row": 8928316  },317  {318   "path": "scripts/nemo/hyperparam_tuning/finetune_architecture.py",319   "sha256": "eedae5180c0ce2d58f1fd4269179694f9e36edaaffc59b90ec6353d960928c6a",320   "language": "Python",321   "lines": 421,322   "truncated": false,323   "block": 1,324   "row": 9118325  },326  {327   "path": "scripts/nemo/hyperparam_tuning/finetune_learning.py",328   "sha256": "aec4710efcc167d358209aa13992a204701015659c9574746b9c7ebe4ea3b799",329   "language": "Python",330   "lines": 340,331   "truncated": false,332   "block": 1,333   "row": 8897334  },335  {336   "path": "scripts/nemo/hyperparam_tuning/get_completed_trials.py",337   "sha256": "56249b6cb27736c77e7943839de24e29f023f01fe75b1793e47c0d3a10df004c",338   "language": "Python",339   "lines": 43,340   "truncated": false,341   "block": 1,342   "row": 6194343  },344  {345   "path": "scripts/nemo/hyperparam_tuning/optimize_architecture.py",346   "sha256": "38b7a118a8a48deba686a9d3790373828ad054ec0877a275a997c096c4534a9d",347   "language": "Python",348   "lines": 503,349   "truncated": false,350   "block": 1,351   "row": 9362352  },353  {354   "path": "scripts/nemo/hyperparam_tuning/optimize_learning.py",355   "sha256": "643cc9d96cf12e8a1316e7bd4277143098715c849f488377ab34abcf8d5ca9fd",356   "language": "Python",357   "lines": 331,358   "truncated": false,359   "block": 1,360   "row": 8878361  },362  {363   "path": "scripts/nemo/hyperparam_tuning/validate_architecture.py",364   "sha256": "2bbd05a40d085a7d81653029afa0c96cef19c4275c3f8426e226a1c09a23cebc",365   "language": "Python",366   "lines": 426,367   "truncated": false,368   "block": 1,369   "row": 9038370  },371  {372   "path": "scripts/nemo/model_stats.py",373   "sha256": "752a641d75a6b368fd3e5f18271dd69ce48a5c76b7050889a02bfd8f2a18307d",374   "language": "Python",375   "lines": 51,376   "truncated": false,377   "block": 1,378   "row": 6261379  },380  {381   "path": "scripts/nemo/mutation/mutate_sequences.py",382   "sha256": "97a407ac864da7bf5c9989c42e90beb4ee22ea8f68e88fc0789e28d9c27e8630",383   "language": "Python",384   "lines": 247,385   "truncated": false,386   "block": 1,387   "row": 8714388  },389  {390   "path": "scripts/nemo/preprocessing/clean_up_expression_matrix.R",391   "sha256": "73dcad901557c0f08d2c04ff0f68f3aae1c019b12e570e9e59e61eb50b0bfaf5",392   "language": "R",393   "lines": 75,394   "truncated": false,395   "block": 1,396   "row": 10149397  },398  {399   "path": "scripts/nemo/preprocessing/csv_to_fasta.py",400   "sha256": "e7cfb0ebb36c752b279f00ba0a36158dccb88dc24a826f7a3a604a145ec57b2f",401   "language": "Python",402   "lines": 97,403   "truncated": false,404   "block": 1,405   "row": 7187406  },407  {408   "path": "scripts/nemo/preprocessing/downsample_data.py",409   "sha256": "8122ef5ba8078bdac803a6983416c5666a92e63fa3aa90b3610e5cd9112e4c71",410   "language": "Python",411   "lines": 60,412   "truncated": false,413   "block": 1,414   "row": 6512415  },416  {417   "path": "scripts/nemo/preprocessing/get_len_gc.py",418   "sha256": "bbecd534f24d3c15ab004b325248605897ea1aa37bd8f873140fc11e3be1fbd3",419   "language": "Python",420   "lines": 98,421   "truncated": false,422   "block": 1,423   "row": 6936424  },425  {426   "path": "scripts/nemo/preprocessing/get_median.R",427   "sha256": "7cc21def3555785be0008e538ff3108b7b41acc566ee213404d854f6b645e882",428   "language": "R",429   "lines": 71,430   "truncated": false,431   "block": 1,432   "row": 10141433  },434  {435   "path": "scripts/nemo/preprocessing/get_promoter_terminator.py",436   "sha256": "71f729f35d4e3a3802ae0c3a5cd53ba60aef1b71d5acb641df6f35a41597370b",437   "language": "Python",438   "lines": 210,439   "truncated": false,440   "block": 1,441   "row": 8532442  },443  {444   "path": "scripts/nemo/preprocessing/get_rep_avrg.R",445   "sha256": "9aa59bf1f36c4176caf100cdc15cf9b0d8967e459912d03b9897075a4f40bd61",446   "language": "R",447   "lines": 67,448   "truncated": false,449   "block": 1,450   "row": 10142451  },452  {453   "path": "scripts/nemo/preprocessing/gff2bed.py",454   "sha256": "551cbc938e8c1e64089a73c52145e438e531724bb5ad241b43a056cece72b43e",455   "language": "Python",456   "lines": 47,457   "truncated": false,458   "block": 1,459   "row": 6287460  },461  {462   "path": "scripts/nemo/preprocessing/graphpart_prep_only_expressed.R",463   "sha256": "3e946e35789431685e3441724f51a16d4ca4a0e23f7cf527ea0bc697c91bfbe9",464   "language": "R",465   "lines": 106,466   "truncated": false,467   "block": 1,468   "row": 10261469  },470  {471   "path": "scripts/nemo/preprocessing/merge_data.py",472   "sha256": "3c4ef15046cb91abad90d435b9c8fee5abd9489e4ce5ec2320e81d6cacb8aa7a",473   "language": "Python",474   "lines": 304,475   "truncated": false,476   "block": 1,477   "row": 8590478  },479  {480   "path": "scripts/nemo/preprocessing/multiline_to_singleline_fasta.sh",481   "sha256": "cc7d60c24de302ab19da435ac84e6e79b1e6c87a6280230217a20d6f7cd23f6a",482   "language": "Shell",483   "lines": 44,484   "truncated": false,485   "block": 1,486   "row": 11671487  },488  {489   "path": "scripts/nemo/preprocessing/remove_low_corr_samples.R",490   "sha256": "41ca403ac28e85827c3c9fd70c5765e33e9d82bd175f59224f7f94371866d4e7",491   "language": "R",492   "lines": 92,493   "truncated": false,494   "block": 1,495   "row": 10163496  },497  {498   "path": "scripts/nemo/preprocessing/setup_folds.py",499   "sha256": "6dc7c67ada511bdd7c39a0b663b91801be04df17834041f3f020ded697c00fd8",500   "language": "Python",501   "lines": 234,502   "truncated": false,503   "block": 1,504   "row": 8517505  },506  {507   "path": "scripts/nemo/preprocessing/setup_full.py",508   "sha256": "37179634a572588a46a7fec5aa440d4a78e56cc7202cbe595895b1b6ffd3bb09",509   "language": "Python",510   "lines": 118,511   "truncated": false,512   "block": 1,513   "row": 7203514  },515  {516   "path": "scripts/nemo/preprocessing/shuffle_graphpart_clusters.py",517   "sha256": "afbd8d0c1b5684733838cf312b39700ef23b90a757d735e3ae9f8be18536e55d",518   "language": "Python",519   "lines": 49,520   "truncated": false,521   "block": 1,522   "row": 6342523  },524  {525   "path": "scripts/nemo/run_training.py",526   "sha256": "314aad2778335f42c7c2df029f89682556492a335ec64f24b36670f98f788360",527   "language": "Python",528   "lines": 430,529   "truncated": false,530   "block": 1,531   "row": 9106532  },533  {534   "path": "scripts/nemo/utils/attrib_utils.py",535   "sha256": "a25a733da12e30bb48ab4693cd69e46598fbbb03b657ad1238564b206fa695a4",536   "language": "Python",537   "lines": 279,538   "truncated": false,539   "block": 1,540   "row": 8841541  },542  {543   "path": "scripts/nemo/utils/eval_utils.R",544   "sha256": "fb98b30955067257f417da3a3c03456272c4561155d68bcd235978902fb50d5c",545   "language": "R",546   "lines": 90,547   "truncated": false,548   "block": 1,549   "row": 10168550  },551  {552   "path": "scripts/nemo/utils/model_utils.py",553   "sha256": "fe893961c963532939f030f58a92a7bd719dfeeced91831095468026cfc14f7c",554   "language": "Python",555   "lines": 678,556   "truncated": false,557   "block": 1,558   "row": 9538559  },560  {561   "path": "scripts/prep_Athaliana.sh",562   "sha256": "be867226f8840d46e9ce40011ef3441ae86ae06972e55a4de96adb6400a3d327",563   "language": "Shell",564   "lines": 163,565   "truncated": false,566   "block": 1,567   "row": 11741568  },569  {570   "path": "scripts/prep_Bnapus.sh",571   "sha256": "eb64bc4fd3f243e0337f706b51e49f9066fb2b153eb3ee2383d140c0f378094e",572   "language": "Shell",573   "lines": 174,574   "truncated": false,575   "block": 1,576   "row": 11743577  },578  {579   "path": "scripts/run_setup.sh",580   "sha256": "c8ab43614e647ab973b2bf1db1855dacbfec9695de1ce2f1f928b4f0ff4636ca",581   "language": "Shell",582   "lines": 101,583   "truncated": false,584   "block": 1,585   "row": 11718586  },587  {588   "path": "scripts/setup_files.sh",589   "sha256": "50ca22e7b9a325d15ea385c9271278199c61c4b8d9e09eb9b959799c2e372bd2",590   "language": "Shell",591   "lines": 221,592   "truncated": false,593   "block": 1,594   "row": 11746595  },596  {597   "path": "scripts/train.sh",598   "sha256": "16b87f2f2e7390a52784bd66307dbc7963bda775ef00f86a9e9172297def4820",599   "language": "Shell",600   "lines": 77,601   "truncated": false,602   "block": 1,603   "row": 11700604  },605  {606   "path": "scripts/train_Athaliana.sh",607   "sha256": "194fce5c201ff7f6418bb49600b4c4f92a458271462e85370776115c131fd14b",608   "language": "Shell",609   "lines": 56,610   "truncated": false,611   "block": 1,612   "row": 11673613  },614  {615   "path": "scripts/train_Bnapus.sh",616   "sha256": "258b2892b0c0626be66612e597ebb9b4ca7cf29fbdb68c8c1025468755648047",617   "language": "Shell",618   "lines": 80,619   "truncated": false,620   "block": 1,621   "row": 11701622  },623  {624   "path": "scripts/tune_hyperparams.sh",625   "sha256": "98173bee60b4e18729af9282ed7f82faa40e07878471294bc54554819bc4a071",626   "language": "Shell",627   "lines": 96,628   "truncated": false,629   "block": 1,630   "row": 11722631  }632 ]633}