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/seqscope/novascope-exemplary-downstream-analysis",4 "url": "https://github.com/seqscope/NovaScope-exemplary-downstream-analysis",5 "host": "github.com",6 "commit": "af9f3696b0ebc825fcb8b82abcc2a387bebc00c0",7 "license": "Apache-2.0",8 "license_confirmed_by": "license file LICENSE",9 "redistribution": "yes",10 "files": [11 {12 "path": "LICENSE",13 "sha256": "c71d239df91726fc519c6eb72d318ec65820627232b2f796219e87dcf35d0ab4",14 "language": "License",15 "lines": 201,16 "truncated": false,17 "block": 1,18 "row": 221619 },20 {21 "path": "README.md",22 "sha256": "63e5230ef646571b55047bb1739090afea04fa4aab7accc2d29bde12fc26fcae",23 "language": "Text",24 "lines": 9,25 "truncated": false,26 "block": 13,27 "row": 611428 },29 {30 "path": "scripts/check_and_link_file.py",31 "sha256": "c8b6170b200b3aa7a8348a8a31c16c259fdecff05ee06f5652580461c9849866",32 "language": "Python",33 "lines": 46,34 "truncated": false,35 "block": 12,36 "row": 801537 },38 {39 "path": "scripts/make_segmask.py",40 "sha256": "77af8b2eff1bbbddc6979b9c2962fdb40f475954bf19334538c1a9f887c6efbc",41 "language": "Python",42 "lines": 51,43 "truncated": false,44 "block": 12,45 "row": 855746 },47 {48 "path": "scripts/make_sge_from_npy.py",49 "sha256": "ae24cf658c753495121f92fe9d0698a7d634eb42a5f1523d1d395f2b64fd3fbf",50 "language": "Python",51 "lines": 143,52 "truncated": false,53 "block": 12,54 "row": 1591955 },56 {57 "path": "scripts/process_input.sh",58 "sha256": "ae189342e38cefdd6c58f2557617e2246bd6048662cd8662ee61d030a1888951",59 "language": "Shell",60 "lines": 132,61 "truncated": false,62 "block": 13,63 "row": 566864 },65 {66 "path": "scripts/seurat_analysis.R",67 "sha256": "f63d10e7317fc3cc7719abd979c59ff895da4c51a256dc92e13499446eae8eac",68 "language": "R",69 "lines": 418,70 "truncated": false,71 "block": 13,72 "row": 307373 },74 {75 "path": "scripts/seurat_analysis_viz.R",76 "sha256": "bd9a35f695660a198a1e8a631ff3aafac4951bef407c517d4222fdaaedd2fa2c",77 "language": "R",78 "lines": 166,79 "truncated": false,80 "block": 13,81 "row": 232682 },83 {84 "path": "scripts/seurat_cluster_to_count_matrix_for_categorical.py",85 "sha256": "f0b54db703815e4d0e19beced1c5bfc5bbd26ac209f29f2cfba7d851d52baad1",86 "language": "Python",87 "lines": 83,88 "truncated": false,89 "block": 12,90 "row": 1117691 },92 {93 "path": "site/assets/javascripts/bundle.c8d2eff1.min.js",94 "sha256": "7d80237cb0c156056172f1da7543d6fce43a86612ce1a338440e96405a5be603",95 "language": "JavaScript",96 "lines": 29,97 "truncated": false,98 "block": 11,99 "row": 11544100 },101 {102 "path": "site/assets/javascripts/lunr/min/lunr.ar.min.js",103 "sha256": "89a1dcb094a8491d968c151ab254a03195c87ff2adaa2408c769928284847125",104 "language": "JavaScript",105 "lines": 1,106 "truncated": false,107 "block": 5,108 "row": 15221109 },110 {111 "path": "site/assets/javascripts/lunr/min/lunr.da.min.js",112 "sha256": "2a12734048eae74e0a05e5c108fdf24c2b71dfcd8da712336ca9e3d27ab92956",113 "language": "JavaScript",114 "lines": 18,115 "truncated": false,116 "block": 5,117 "row": 14801118 },119 {120 "path": "site/assets/javascripts/lunr/min/lunr.de.min.js",121 "sha256": "bcaa7c5c19bc730c05bb91e22ae0e386e1ac4a0580c42b7d94f9b8757aadadab",122 "language": "JavaScript",123 "lines": 18,124 "truncated": false,125 "block": 5,126 "row": 14895127 },128 {129 "path": "site/assets/javascripts/lunr/min/lunr.du.min.js",130 "sha256": "452da04fe449b9c65c61384fec582dc63824bd4e559fae2c3926a7790b68e976",131 "language": "JavaScript",132 "lines": 18,133 "truncated": false,134 "block": 5,135 "row": 14900136 },137 {138 "path": "site/assets/javascripts/lunr/min/lunr.el.min.js",139 "sha256": "a6fd5cbbb21d127407bc31c6c4298bf92ec7e1496a1ea83d5e4add14325a0c21",140 "language": "JavaScript",141 "lines": 1,142 "truncated": false,143 "block": 5,144 "row": 15185145 },146 {147 "path": "site/assets/javascripts/lunr/min/lunr.es.min.js",148 "sha256": "dec4ec90bd6f478ca3e65636a8e3fedf512b23d01a51a01d7e7822f67ebbaaf8",149 "language": "JavaScript",150 "lines": 18,151 "truncated": false,152 "block": 5,153 "row": 15115154 },155 {156 "path": "site/assets/javascripts/lunr/min/lunr.fi.min.js",157 "sha256": "681541fcf5b1987ad8b00766e9c06389ecf99c3d7ae817fa891f923f691b8668",158 "language": "JavaScript",159 "lines": 18,160 "truncated": false,161 "block": 5,162 "row": 15046163 },164 {165 "path": "site/assets/javascripts/lunr/min/lunr.fr.min.js",166 "sha256": "4dd56aa2551e770ad26ef4b85092cd31447671e0e84b39514278547f54177377",167 "language": "JavaScript",168 "lines": 18,169 "truncated": false,170 "block": 5,171 "row": 15086172 },173 {174 "path": "site/assets/javascripts/lunr/min/lunr.he.min.js",175 "sha256": "3f7d5c28ada94d78c9bc8041e271c355800ba36dbab98ad95d57b6bc25993621",176 "language": "JavaScript",177 "lines": 1,178 "truncated": false,179 "block": 5,180 "row": 14951181 },182 {183 "path": "site/assets/javascripts/lunr/min/lunr.hi.min.js",184 "sha256": "631fff52e3623f2dfba35af076c6b8b5a450eeffe30a5cfac7458dab77cbe0a6",185 "language": "JavaScript",186 "lines": 1,187 "truncated": false,188 "block": 5,189 "row": 14698190 },191 {192 "path": "site/assets/javascripts/lunr/min/lunr.hu.min.js",193 "sha256": "876c969bbf4a2b84738f4e0a14922ee331cb7c2193a621f65db7f836fdd33a38",194 "language": "JavaScript",195 "lines": 18,196 "truncated": false,197 "block": 5,198 "row": 15049199 },200 {201 "path": "site/assets/javascripts/lunr/min/lunr.hy.min.js",202 "sha256": "0efbcb902bdb7ec0dddffa5e2ba347b74c49ffc5f43fd73ffed83528eba12e95",203 "language": "JavaScript",204 "lines": 1,205 "truncated": false,206 "block": 5,207 "row": 14370208 },209 {210 "path": "site/assets/javascripts/lunr/min/lunr.it.min.js",211 "sha256": "00a5073df2e922e5fded1c5a4d4011aec02472ab9d9182a7c6508d60b625c453",212 "language": "JavaScript",213 "lines": 18,214 "truncated": false,215 "block": 5,216 "row": 15104217 },218 {219 "path": "site/assets/javascripts/lunr/min/lunr.ja.min.js",220 "sha256": "c4fded308f633681a6ed53b6c10d8ca5916fdfd50f6b82ec914d725be0cb8bd6",221 "language": "JavaScript",222 "lines": 1,223 "truncated": false,224 "block": 5,225 "row": 14563226 },227 {228 "path": "site/assets/javascripts/lunr/min/lunr.jp.min.js",229 "sha256": "04114edc36dc114edce5afbb3c7f795f45c77d8673c1edcdca5675ddab5d5199",230 "language": "JavaScript",231 "lines": 1,232 "truncated": false,233 "block": 5,234 "row": 13649235 },236 {237 "path": "site/assets/javascripts/lunr/min/lunr.kn.min.js",238 "sha256": "a064d0d7438334957a442b626140fb72f4ede8ebe17eb5c4e25682d87c88bbf8",239 "language": "JavaScript",240 "lines": 1,241 "truncated": false,242 "block": 5,243 "row": 14713244 },245 {246 "path": "site/assets/javascripts/lunr/min/lunr.ko.min.js",247 "sha256": "73d1bdb1de4aef6c5920f516924c5ab1c440db50a6f5c6126bd0fb7cf5d37664",248 "language": "JavaScript",249 "lines": 1,250 "truncated": false,251 "block": 5,252 "row": 14994253 },254 {255 "path": "site/assets/javascripts/lunr/min/lunr.multi.min.js",256 "sha256": "9761f475ae79f36420ff714df9950efb264effcf9230efd55b511a0de899e979",257 "language": "JavaScript",258 "lines": 1,259 "truncated": false,260 "block": 5,261 "row": 14130262 },263 {264 "path": "site/assets/javascripts/lunr/min/lunr.nl.min.js",265 "sha256": "399ef26d61ed2d5806f58ea723dfaca09f4a7c9b51e315bdd17482c8e3013a3e",266 "language": "JavaScript",267 "lines": 18,268 "truncated": false,269 "block": 5,270 "row": 14891271 },272 {273 "path": "site/assets/javascripts/lunr/min/lunr.no.min.js",274 "sha256": "57f9db9290f9ed36080755f53ee342a04f55a5954e4add915d1c301a37464573",275 "language": "JavaScript",276 "lines": 18,277 "truncated": false,278 "block": 5,279 "row": 14812280 },281 {282 "path": "site/assets/javascripts/lunr/min/lunr.pt.min.js",283 "sha256": "3a25d2abaa23063cf13fc56c19ae4cc5050cb6215115e9d08f4a6f4b78780067",284 "language": "JavaScript",285 "lines": 18,286 "truncated": false,287 "block": 5,288 "row": 15069289 },290 {291 "path": "site/assets/javascripts/lunr/min/lunr.ro.min.js",292 "sha256": "cfa26a8ea4293d81e8547ba2321d703a0fe9881f0721fca5f33a3f80bf156ee9",293 "language": "JavaScript",294 "lines": 18,295 "truncated": false,296 "block": 5,297 "row": 15091298 },299 {300 "path": "site/assets/javascripts/lunr/min/lunr.ru.min.js",301 "sha256": "50ef3c0fab4a3f2d260e8973c63363aa0dcf02b559ea9d11d5f02b6197585c17",302 "language": "JavaScript",303 "lines": 18,304 "truncated": false,305 "block": 5,306 "row": 15074307 },308 {309 "path": "site/assets/javascripts/lunr/min/lunr.sa.min.js",310 "sha256": "41c558a4355c3eae8f0a27ae870712738f14b0bd88038042ac8ab8b411e5817f",311 "language": "JavaScript",312 "lines": 1,313 "truncated": false,314 "block": 5,315 "row": 14824316 },317 {318 "path": "site/assets/javascripts/lunr/min/lunr.stemmer.support.min.js",319 "sha256": "2e7213605846a18014ec750910cb18a8a4c60bb23200103b3fad9ef27b10c705",320 "language": "JavaScript",321 "lines": 1,322 "truncated": false,323 "block": 5,324 "row": 14722325 },326 {327 "path": "site/assets/javascripts/lunr/min/lunr.sv.min.js",328 "sha256": "942b165bcc8218e3246fc4735af9b1c2f66514366d0000be051bf1bb896d413e",329 "language": "JavaScript",330 "lines": 18,331 "truncated": false,332 "block": 5,333 "row": 14794334 },335 {336 "path": "site/assets/javascripts/lunr/min/lunr.ta.min.js",337 "sha256": "17a32dc49c27c9d27945625a7e8d066d42f64ea1ce5a5b34de427723fbf9ae2a",338 "language": "JavaScript",339 "lines": 1,340 "truncated": false,341 "block": 5,342 "row": 14577343 },344 {345 "path": "site/assets/javascripts/lunr/min/lunr.te.min.js",346 "sha256": "079c8fcf028aeef388e98ec8607c8ea50ba9660c46797c8a119d05f8f8205838",347 "language": "JavaScript",348 "lines": 1,349 "truncated": false,350 "block": 5,351 "row": 14566352 },353 {354 "path": "site/assets/javascripts/lunr/min/lunr.th.min.js",355 "sha256": "348461266843e316b26820004a96d3fd87a1579829d244ce510c17293eef0439",356 "language": "JavaScript",357 "lines": 1,358 "truncated": false,359 "block": 5,360 "row": 14288361 },362 {363 "path": "site/assets/javascripts/lunr/min/lunr.tr.min.js",364 "sha256": "e8bf57b1033b8bd92ea04a94c533015aa1a7f0a8d6830194b974e94e1e4aca3c",365 "language": "JavaScript",366 "lines": 18,367 "truncated": false,368 "block": 5,369 "row": 15186370 },371 {372 "path": "site/assets/javascripts/lunr/min/lunr.vi.min.js",373 "sha256": "2e39c3fd7305f6e66fc0424796a7696cb8e36dc0f5c3a83ea1bc44dfe3fecb56",374 "language": "JavaScript",375 "lines": 1,376 "truncated": false,377 "block": 5,378 "row": 14103379 },380 {381 "path": "site/assets/javascripts/lunr/min/lunr.zh.min.js",382 "sha256": "d8c5b72c36ec9c3197602546e9ba5b57ada3f725d564a551bf16eabafb548e88",383 "language": "JavaScript",384 "lines": 1,385 "truncated": false,386 "block": 5,387 "row": 14540388 },389 {390 "path": "site/assets/javascripts/lunr/tinyseg.js",391 "sha256": "1b044c239610ef65fceff6039567442bb1692d413f5ee8686fee81b1a3067761",392 "language": "JavaScript",393 "lines": 206,394 "truncated": false,395 "block": 5,396 "row": 15304397 },398 {399 "path": "site/assets/javascripts/lunr/wordcut.js",400 "sha256": "7d2c264191b83d37a9c4e48276d0e2b076b5e5d5f225bc18ead1e8c54d009405",401 "language": "JavaScript",402 "lines": 186,403 "truncated": true,404 "block": 5,405 "row": 15600406 },407 {408 "path": "site/assets/javascripts/workers/search.b8dbb3d2.min.js",409 "sha256": "10ecd830dcb35afd01aca140279cb8c84ac07f7ed17e9106b783a021b885301a",410 "language": "JavaScript",411 "lines": 42,412 "truncated": false,413 "block": 11,414 "row": 11525415 },416 {417 "path": "site/js/open_in_new_tab.js",418 "sha256": "2d86a61e005fa4b9211065cfbbcf2b8ec11a7410ed027c26e062f4f23deb07d9",419 "language": "JavaScript",420 "lines": 45,421 "truncated": false,422 "block": 11,423 "row": 11116424 },425 {426 "path": "steps/step1-create-minibatch.sh",427 "sha256": "bbdd4fecacf61a10a2da22efd4ae952769e6dfc1b7560cd088643cb13895d648",428 "language": "Shell",429 "lines": 59,430 "truncated": false,431 "block": 13,432 "row": 5213433 },434 {435 "path": "steps/step2a.1-LDA-factorization.sh",436 "sha256": "6a29b9d3791026adfe6c0a9c203104fd48282554aa7ba523240498db00dbcbd2",437 "language": "Shell",438 "lines": 53,439 "truncated": false,440 "block": 13,441 "row": 5169442 },443 {444 "path": "steps/step2a.2-LDA-factorization-report.sh",445 "sha256": "1c8e9d4aa9b4c46c18fa315b07a124c7b3c96828e73d986ef8916567075dd8dc",446 "language": "Shell",447 "lines": 68,448 "truncated": false,449 "block": 13,450 "row": 5299451 },452 {453 "path": "steps/step2b.1-Seurat-test-cutoff.sh",454 "sha256": "2125442804b4a12f9c8264fa112dcde7379d8c30ec005b829934e3a7c20ac0e6",455 "language": "Shell",456 "lines": 50,457 "truncated": false,458 "block": 13,459 "row": 5126460 },461 {462 "path": "steps/step2b.3-Seurat-clustering.sh",463 "sha256": "df583e16f01982c7f2ae5ce5740366953f0373d80ce69669e995733ec1a4f41c",464 "language": "Shell",465 "lines": 56,466 "truncated": false,467 "block": 13,468 "row": 5237469 },470 {471 "path": "steps/step2b.5-Seurat-count-matrix.sh",472 "sha256": "d924ca605a7468af056e8ba36117c1393a2b6b678c41075edb174880ad7dbe4d",473 "language": "Shell",474 "lines": 89,475 "truncated": false,476 "block": 13,477 "row": 5515478 },479 {480 "path": "steps/step3.1-transform.sh",481 "sha256": "6a6714f5db6d83c77c93931818fd01995a6950168602e66b23def6f8ac5ea157",482 "language": "Shell",483 "lines": 71,484 "truncated": false,485 "block": 13,486 "row": 5385487 },488 {489 "path": "steps/step3.2-transform-visualization.sh",490 "sha256": "5abea7e5f94d5baab8e87c02f5a2e5ce79dc45c216f5acca49b4a6a4ed6d3f90",491 "language": "Shell",492 "lines": 96,493 "truncated": false,494 "block": 13,495 "row": 5465496 },497 {498 "path": "steps/step4.1-pixel-level-decode.sh",499 "sha256": "44b2312e7d1f3ef92057b1ae91fa4c8a665701ed64050a1d057b621e94d301fb",500 "language": "Shell",501 "lines": 116,502 "truncated": false,503 "block": 13,504 "row": 5594505 },506 {507 "path": "steps/step4.2-pixel-level-visualization-and-report.sh",508 "sha256": "8e6c4ee2fa689bd72f96496b61bd0aa8778ea7a747462b224650f97ec091495c",509 "language": "Shell",510 "lines": 77,511 "truncated": false,512 "block": 13,513 "row": 5406514 }515 ]516}