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.
05.6k
1{2 "format": "oscr-script-manifest/1",3 "repository": "github.com/hr1912/tacman",4 "url": "https://github.com/hr1912/TACMAN",5 "host": "github.com",6 "commit": "b8e815fee6057391ea5eb4fe687ccd845f02bee5",7 "license": "MIT",8 "license_confirmed_by": "license file LICENSE",9 "redistribution": "yes",10 "files": [11 {12 "path": "LICENSE",13 "sha256": "eb1104c41b0643d4cfa9a92a7374e687717835eb50bbeefa92dcaf5b6a42fcc6",14 "language": "License",15 "lines": 21,16 "truncated": false,17 "block": 6,18 "row": 182119 },20 {21 "path": "README.md",22 "sha256": "548ce9b801e033f64a8824d3c46f9705c3a8dd9140c08ca6c959b256cea8a6e8",23 "language": "Text",24 "lines": 110,25 "truncated": false,26 "block": 8,27 "row": 1010428 },29 {30 "path": "TACMAN/__init__.py",31 "sha256": "aa1edcad9a3007df6216e28be462f0a1238b0b8185726b0ad35142c6e93a6a58",32 "language": "Python",33 "lines": 10,34 "truncated": false,35 "block": 6,36 "row": 2158037 },38 {39 "path": "TACMAN/args.py",40 "sha256": "43a9329ed9303d167b002a9fd94d8ca77aa52426288f5fa5bccb77e30c14317c",41 "language": "Python",42 "lines": 63,43 "truncated": false,44 "block": 6,45 "row": 3721546 },47 {48 "path": "TACMAN/model/__init__.py",49 "sha256": "0ca2dcd1c3aef56d04c51d644ffa4961b765e77118c4f209fd02464894775754",50 "language": "Python",51 "lines": 1,52 "truncated": false,53 "block": 6,54 "row": 2029455 },56 {57 "path": "TACMAN/model/baselayer.py",58 "sha256": "f5252ddbfc0eb124209a8cf3578a0c7e86544f4a9906f1676262a4b9a4682ab6",59 "language": "Python",60 "lines": 227,61 "truncated": false,62 "block": 7,63 "row": 191164 },65 {66 "path": "TACMAN/model/model.py",67 "sha256": "290e4a0c44488254a32c2dfda251bfa60b8fa459d9c7b1e33b5800aa59f4163f",68 "language": "Python",69 "lines": 212,70 "truncated": false,71 "block": 7,72 "row": 66973 },74 {75 "path": "TACMAN/utils/MNN.py",76 "sha256": "8f8f5b2c34f38250bd2e4cd6660285134c489de1134bf76bc7a2135e008d97fb",77 "language": "Python",78 "lines": 123,79 "truncated": false,80 "block": 6,81 "row": 3999882 },83 {84 "path": "TACMAN/utils/ResourceRecord.py",85 "sha256": "e2888f47026febacdbbcbe3104e418bc06134bcf2653da82d35b05faffc4d3dd",86 "language": "Python",87 "lines": 53,88 "truncated": false,89 "block": 6,90 "row": 2856091 },92 {93 "path": "TACMAN/utils/args.py",94 "sha256": "43a9329ed9303d167b002a9fd94d8ca77aa52426288f5fa5bccb77e30c14317c",95 "language": "Python",96 "lines": 63,97 "truncated": false,98 "block": 6,99 "row": 37215100 },101 {102 "path": "TACMAN/utils/arr.py",103 "sha256": "591f8606239f6fe1579f589b2cd480284d167e10cebae4c420cce58d749ed56a",104 "language": "Python",105 "lines": 85,106 "truncated": false,107 "block": 6,108 "row": 32560109 },110 {111 "path": "TACMAN/utils/df.py",112 "sha256": "444e535bddd1a27e36a9eedc82c836d4a34c85ff0fc7d4baaf09c1699f5995e6",113 "language": "Python",114 "lines": 362,115 "truncated": false,116 "block": 7,117 "row": 3661118 },119 {120 "path": "TACMAN/utils/eval.py",121 "sha256": "7f69b276eda9f0ce7da480ca1204bf36d0377e44e4ee4bde89171aef6cfd75cc",122 "language": "Python",123 "lines": 22,124 "truncated": false,125 "block": 6,126 "row": 23550127 },128 {129 "path": "TACMAN/utils/general.py",130 "sha256": "faac21cb843811accff1bc8c43ac97888dce8c792ba3058da8eaf343ac68a89c",131 "language": "Python",132 "lines": 609,133 "truncated": false,134 "block": 7,135 "row": 8625136 },137 {138 "path": "TACMAN/utils/loss.py",139 "sha256": "4833f275f47b754ba8c72b864ea7e575f833ed277c1fc31737264fbc0d7eafa3",140 "language": "Python",141 "lines": 18,142 "truncated": false,143 "block": 6,144 "row": 23452145 },146 {147 "path": "TACMAN/utils/plot/__init__.py",148 "sha256": "db14dc9c2d0f1062ea293a7aa4da3b701805ad4d71bc7bd2bb7531c1f589d350",149 "language": "Python",150 "lines": 53,151 "truncated": false,152 "block": 6,153 "row": 24597154 },155 {156 "path": "TACMAN/utils/plot/cmap.py",157 "sha256": "88efd7db57b1a50b251fb112df3a6bac7349527494db81ada3d0a06b2cb3343c",158 "language": "Python",159 "lines": 154,160 "truncated": false,161 "block": 6,162 "row": 42370163 },164 {165 "path": "TACMAN/utils/plot/figure.py",166 "sha256": "84e3e3cacdafb595e408d07f76e3557d622cebc65d8682f579cfa3bd0c805f9f",167 "language": "Python",168 "lines": 629,169 "truncated": false,170 "block": 7,171 "row": 8157172 },173 {174 "path": "TACMAN/utils/plot/path.py",175 "sha256": "7e1c3a1541dc619faf76d3793ae275880cbaf5f6b174275cb897b0fdc263c100",176 "language": "Python",177 "lines": 46,178 "truncated": false,179 "block": 6,180 "row": 23311181 },182 {183 "path": "TACMAN/utils/plot/pl.py",184 "sha256": "4baa833dd61ed1858d2cafd35f5319ff9efa15098d2f36482ebce4064e50c1cc",185 "language": "Python",186 "lines": 910,187 "truncated": false,188 "block": 7,189 "row": 10563190 },191 {192 "path": "TACMAN/utils/preprocess.py",193 "sha256": "86908275dd28ead159dab7238d7e904047ac13a0f06afcf8afff92fc53e5b781",194 "language": "Python",195 "lines": 1010,196 "truncated": false,197 "block": 7,198 "row": 11428199 },200 {201 "path": "TACMAN/utils/train.py",202 "sha256": "f67dcba82bbb4c3cdc89b713fa26436716990e45487fb2801a23402108d1644a",203 "language": "Python",204 "lines": 440,205 "truncated": false,206 "block": 7,207 "row": 8056208 },209 {210 "path": "TACMAN/utils/utility.py",211 "sha256": "2834b93911837ecba75b9064369544999d164119cfc676e004409cf8bd836192",212 "language": "Python",213 "lines": 178,214 "truncated": false,215 "block": 6,216 "row": 42200217 },218 {219 "path": "benchmark/cell_annotation_HCL.ipynb",220 "sha256": "5f5ebcc32f51543c754674dd0b1cd193fd0c79c03e0a3b6f2dfa07b7e8faffc1",221 "language": "Jupyter",222 "lines": 87,223 "truncated": false,224 "block": 5,225 "row": 16292226 },227 {228 "path": "benchmark/cell_annotation_MCA.ipynb",229 "sha256": "a1ba1a4646bdb4453bf2cb445289cc5f7de97f68f9a6d4dfe1cf295b39651408",230 "language": "Jupyter",231 "lines": 88,232 "truncated": false,233 "block": 5,234 "row": 16289235 },236 {237 "path": "benchmark/plot.py",238 "sha256": "0acfaaccc155bdb0409ce0e2b02ff8a8b2fd5cddd7d19db50dba9c77f721862a",239 "language": "Python",240 "lines": 339,241 "truncated": false,242 "block": 7,243 "row": 3638244 },245 {246 "path": "benchmark/script/extract_url.py",247 "sha256": "a0c78b2b254c6657db8f173cc9cbb185b053ba6e259df7dd2645155e92b84761",248 "language": "Python",249 "lines": 93,250 "truncated": false,251 "block": 6,252 "row": 33486253 },254 {255 "path": "benchmark/script/fun_three_model.py",256 "sha256": "f9d35af2458b77b3647749dafa0b8158bbed122daf6d63c3be933ff6905aad01",257 "language": "Python",258 "lines": 2771,259 "truncated": false,260 "block": 8,261 "row": 909262 },263 {264 "path": "benchmark/script/init_TACTiCS.py",265 "sha256": "ba84063efc6f81fbb5e7b579fdcd52405fc403ef1af365d7318eb48a46c7f906",266 "language": "Python",267 "lines": 64,268 "truncated": false,269 "block": 6,270 "row": 31855271 },272 {273 "path": "benchmark/script/map_seurat.r",274 "sha256": "f62344c6488131d89fe524f5ee957acb2ce69cf2fd53d9ebef83f02177cebff1",275 "language": "R",276 "lines": 877,277 "truncated": false,278 "block": 8,279 "row": 4926280 },281 {282 "path": "benchmark/script/merge_adatas.py",283 "sha256": "ebf7690b5a080a71b0eb6a4cd4ea3a6a95e581ebc5973bca61e1f200af76b09c",284 "language": "Python",285 "lines": 162,286 "truncated": false,287 "block": 6,288 "row": 40397289 },290 {291 "path": "benchmark/script/utils/__init__.py",292 "sha256": "936290f4071113b396e60869b287ddd2db0329b041e92433f4d9e0f4596ec48a",293 "language": "Python",294 "lines": 115,295 "truncated": false,296 "block": 6,297 "row": 33295298 },299 {300 "path": "benchmark/script/utils/arr.py",301 "sha256": "04b165466514603e630bb12a029b203954967dcdad9974ffa2f2c39c48a7e67b",302 "language": "Python",303 "lines": 84,304 "truncated": false,305 "block": 6,306 "row": 33135307 },308 {309 "path": "benchmark/script/utils/crawl.py",310 "sha256": "8c8503b1f5d8d9c8dd1b1ca7cce6e51d1177636f3f7e0f324baf1eb350b855b1",311 "language": "Python",312 "lines": 85,313 "truncated": false,314 "block": 6,315 "row": 31206316 },317 {318 "path": "benchmark/script/utils/del_py.py",319 "sha256": "aefe4e649f68a47ae0bdf5527020fb9248f74c8ee58a591eda05d1ba1a8ffaca",320 "language": "Python",321 "lines": 84,322 "truncated": false,323 "block": 6,324 "row": 30055325 },326 {327 "path": "benchmark/script/utils/df.py",328 "sha256": "a734096308a8e95707f4559a36038e6a989bfbc631d5605368b55cdfdd055ea3",329 "language": "Python",330 "lines": 396,331 "truncated": false,332 "block": 7,333 "row": 3778334 },335 {336 "path": "benchmark/script/utils/general.py",337 "sha256": "a3f1e9ce1044f5543a8554e0b73beed34ca154188a7d71c6a20a921ba4c1492b",338 "language": "Python",339 "lines": 415,340 "truncated": false,341 "block": 7,342 "row": 3095343 },344 {345 "path": "benchmark/script/utils/nbconvert_ipynb.sh",346 "sha256": "fdf0c50d7f57ebf2fffec431225413f94cf69ddd95f00d0ed146bf9d41915791",347 "language": "Shell",348 "lines": 5,349 "truncated": false,350 "block": 8,351 "row": 6558352 },353 {354 "path": "benchmark/script/utils/plot/__init__.py",355 "sha256": "e5e08c7dbe4b04ef39eacd9174216eb794c1a315b0999ab4d4949866adbeeba3",356 "language": "Python",357 "lines": 52,358 "truncated": false,359 "block": 6,360 "row": 24538361 },362 {363 "path": "benchmark/script/utils/plot/cmap.py",364 "sha256": "3afe5277c0968c1f925f88aec54885f7c55935117081b95709edcf1cd2082fb3",365 "language": "Python",366 "lines": 666,367 "truncated": false,368 "block": 7,369 "row": 10136370 },371 {372 "path": "benchmark/script/utils/plot/figure.py",373 "sha256": "3fae9ad4af6b9cb588f5e8b0d399b757b37baff3e343882cf48dead574232cae",374 "language": "Python",375 "lines": 706,376 "truncated": false,377 "block": 7,378 "row": 8452379 },380 {381 "path": "benchmark/script/utils/plot/path.py",382 "sha256": "ecef73cae7b2f3cff3a472d243be5844c600d8ffd48ffca69a96da6a44c761f1",383 "language": "Python",384 "lines": 48,385 "truncated": false,386 "block": 6,387 "row": 23473388 },389 {390 "path": "benchmark/script/utils/plot/pl.py",391 "sha256": "f3dffe59d707f900cf8e6c3a3e427479201ff3c28c8de1f671e937bae5f93fd5",392 "language": "Python",393 "lines": 917,394 "truncated": false,395 "block": 7,396 "row": 10032397 },398 {399 "path": "benchmark/script/utils/scanpy/__init__.py",400 "sha256": "22b417e503ba4452a38bfcfc2b145df7509e194656750f50fa5c0cd11c1c2304",401 "language": "Python",402 "lines": 27,403 "truncated": false,404 "block": 6,405 "row": 22880406 },407 {408 "path": "benchmark/script/utils/scanpy/pl.py",409 "sha256": "df16b6862249926a7a2182c9c9ebb50140250af9394deeabfe79ef3c3c84b026",410 "language": "Python",411 "lines": 829,412 "truncated": false,413 "block": 7,414 "row": 9335415 },416 {417 "path": "benchmark/script/utils/scanpy/sc.py",418 "sha256": "f18590cb974b3356903a9d9d1d67acdea81c0053acf62ba3c8755501ab8694af",419 "language": "Python",420 "lines": 940,421 "truncated": false,422 "block": 7,423 "row": 10326424 },425 {426 "path": "demo_LC.ipynb",427 "sha256": "802b82a2608386f171b187f410a33b7a9cc469b618b65b113ff128da97cb70ab",428 "language": "Jupyter",429 "lines": 169,430 "truncated": false,431 "block": 5,432 "row": 16760433 },434 {435 "path": "demo_Pancreas.ipynb",436 "sha256": "09f9ace96291ff1616c9cdfdcbdd0edab39df633dc6e62459fc42d10b5b175eb",437 "language": "Jupyter",438 "lines": 165,439 "truncated": false,440 "block": 5,441 "row": 16713442 },443 {444 "path": "examples/homology/celegans_dmelanogaster/download_ensembl115_fasta.sh",445 "sha256": "9377a5210c248611c378bf31f9f5de0180073e0d1298bed6c5a4381a9be30fad",446 "language": "Shell",447 "lines": 13,448 "truncated": false,449 "block": 8,450 "row": 7082451 },452 {453 "path": "examples/homology/celegans_dmelanogaster/run_full_blast_example.sh",454 "sha256": "45ca213e20e733eb9ee1790748d4243f1d3637089566e616526c43b40b5148b0",455 "language": "Shell",456 "lines": 28,457 "truncated": false,458 "block": 8,459 "row": 7861460 },461 {462 "path": "scripts/prepare_homology.optionB_working.py",463 "sha256": "152dfd6c99ec0eab8bd878d964c8b8e58ba1a6348aadf59ab2bc0ac1e07c7779",464 "language": "Python",465 "lines": 551,466 "truncated": false,467 "block": 7,468 "row": 8405469 },470 {471 "path": "scripts/prepare_homology.py",472 "sha256": "fd83ebc41ddfa3b10f01844e113f6270b74be65588663a94b48b9e06acee42e9",473 "language": "Python",474 "lines": 3121,475 "truncated": false,476 "block": 8,477 "row": 1096478 },479 {480 "path": "scripts/run_tacman.py",481 "sha256": "de50a86121cb17add948ed9971f53e24d1b63c6221c3ea3b2f9cb0dcc2e1e1f8",482 "language": "Python",483 "lines": 916,484 "truncated": false,485 "block": 7,486 "row": 11368487 },488 {489 "path": "scripts/summarize_tacman_results.py",490 "sha256": "1c31a5df1f9dd60474bdd819fa70a01dac2ad5cbcc22adfeaf6f61bac30cdec1",491 "language": "Python",492 "lines": 916,493 "truncated": false,494 "block": 7,495 "row": 11325496 },497 {498 "path": "scripts/test_prepare_homology_blast_parser.py",499 "sha256": "06cc0ba35791cf83989801d935a3b3b0b3bf31e333d3bceb6472d91943983121",500 "language": "Python",501 "lines": 247,502 "truncated": false,503 "block": 7,504 "row": 2499505 },506 {507 "path": "scripts/test_prepare_homology_blast_real_ensembl.py",508 "sha256": "8ec714bf4e67a3802521320e44d7a6c69812486b27449024bf94164584606c99",509 "language": "Python",510 "lines": 452,511 "truncated": false,512 "block": 7,513 "row": 6807514 },515 {516 "path": "scripts/test_prepare_homology_config.py",517 "sha256": "7e1a72b805326f6b399a44a517c8979fa2ea80e53f3318f1352740cd4b02f8de",518 "language": "Python",519 "lines": 268,520 "truncated": false,521 "block": 7,522 "row": 2056523 },524 {525 "path": "scripts/test_run_tacman_config.py",526 "sha256": "45068a7f7c81feae3c912f8e429fee28648a933c5576f035b212eb9ccc9cc292",527 "language": "Python",528 "lines": 221,529 "truncated": false,530 "block": 6,531 "row": 44744532 },533 {534 "path": "scripts/test_run_tacman_validation.py",535 "sha256": "325f30de388b603871e8c2edaeada9111120f47238f669d85d14cabbcdeedd5b",536 "language": "Python",537 "lines": 324,538 "truncated": false,539 "block": 7,540 "row": 3624541 },542 {543 "path": "scripts/test_summarize_tacman_results.py",544 "sha256": "2af4f757e8abd12b241949238046fb310e862cf1790cbc6db7d8cacdec387b9e",545 "language": "Python",546 "lines": 288,547 "truncated": false,548 "block": 7,549 "row": 5233550 },551 {552 "path": "scripts/validate_homology.py",553 "sha256": "d36a571660ca762d4cb59adb0e68cc5b0324094be47341e7276b8228078cb27a",554 "language": "Python",555 "lines": 335,556 "truncated": false,557 "block": 7,558 "row": 4092559 }560 ]561}