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/ftwkoopmans/msdap",4 "url": "https://github.com/ftwkoopmans/msdap",5 "host": "github.com",6 "commit": "8af39053b3b0df82601ee63d75eda275b7cedf6a",7 "license": "GPL-3.0",8 "license_confirmed_by": "license file LICENSE",9 "redistribution": "yes",10 "files": [11 {12 "path": "LICENSE",13 "sha256": "3972dc9744f6499f0f9b2dbf76696f2ae7ad8af9b23dde66d6af86c9dfb36986",14 "language": "License",15 "lines": 674,16 "truncated": false,17 "block": 1,18 "row": 223519 },20 {21 "path": "R/dataset.R",22 "sha256": "a625b3440dae3b91d1e83ff06c979766256dc5594b825ec6c1154284dd1b6848",23 "language": "R",24 "lines": 462,25 "truncated": false,26 "block": 10,27 "row": 1882928 },29 {30 "path": "R/dea.R",31 "sha256": "ade6578c41b47b9e3691b74728bed4068d9c2b2712fa4a495a82b4f726d442bd",32 "language": "R",33 "lines": 532,34 "truncated": false,35 "block": 10,36 "row": 1889837 },38 {39 "path": "R/export_data_tables.R",40 "sha256": "547d3367757712960fde49e2995a550a21947e6505a3569ef1f5ee4e8d61d8eb",41 "language": "R",42 "lines": 160,43 "truncated": false,44 "block": 10,45 "row": 1872746 },47 {48 "path": "R/export_stats_genesummary.R",49 "sha256": "b5d3c4be5ba91a3535e140aae061fd78776075e972f7ed073b66a4fcef41e333",50 "language": "R",51 "lines": 401,52 "truncated": false,53 "block": 10,54 "row": 1888155 },56 {57 "path": "R/filter_peptides.R",58 "sha256": "841a94cea4b9aae99a50bb3ca5787ac229bd4a07ddca00c6d08275c0845d0c75",59 "language": "R",60 "lines": 863,61 "truncated": false,62 "block": 10,63 "row": 1893764 },65 {66 "path": "R/gene_idmapping.R",67 "sha256": "fc15f7dad2e563212311a4be20e07ef575cf3b378b32d0ca01a50f2ffa5615c5",68 "language": "R",69 "lines": 377,70 "truncated": false,71 "block": 10,72 "row": 1880473 },74 {75 "path": "R/merge_replicate_samples.R",76 "sha256": "3b6ebf80b4fcacdf485232c647688a44479f48f6ab6ff49f79a1c9aed3e3d818",77 "language": "R",78 "lines": 228,79 "truncated": false,80 "block": 10,81 "row": 1874482 },83 {84 "path": "R/msdap-package.R",85 "sha256": "54d8d82bae7bf27dfb672d2afd71fa48cb497fa3524719977c77e4f797995760",86 "language": "R",87 "lines": 16,88 "truncated": false,89 "block": 10,90 "row": 1789591 },92 {93 "path": "R/msqrobsum__bugfix.R",94 "sha256": "c213579b7e373372279be2ab42c8c9a1241ca43681b405c96f6cf5a77df5ef15",95 "language": "R",96 "lines": 311,97 "truncated": false,98 "block": 10,99 "row": 18794100 },101 {102 "path": "R/normalize_vwmb.R",103 "sha256": "3d00c89560ead02daf11ae598ae24cbf7467dcdefc373009428fad33d5ee65bc",104 "language": "R",105 "lines": 336,106 "truncated": false,107 "block": 10,108 "row": 18805109 },110 {111 "path": "R/parse_encyclopedia.R",112 "sha256": "86a35e333d14e87f4913ce9ff90061ffc545765abc4bc54e9b4d59668757ffb7",113 "language": "R",114 "lines": 177,115 "truncated": false,116 "block": 10,117 "row": 18687118 },119 {120 "path": "R/parse_expressionset.R",121 "sha256": "51738080f178f499ab354d09571abd76dbf0a5be35ef219dc373768308556ad6",122 "language": "R",123 "lines": 84,124 "truncated": false,125 "block": 10,126 "row": 18412127 },128 {129 "path": "R/parse_fragpipe.R",130 "sha256": "0c10aad27dbe21db65cee75f675258f90ceefc6f4bb28498b7d8446abf227e74",131 "language": "R",132 "lines": 600,133 "truncated": false,134 "block": 10,135 "row": 18905136 },137 {138 "path": "R/parse_fragpipe_legacy.R",139 "sha256": "db28b555e4a4eb97aaa0f2c3b6096921a858e95a06e225bd0605915bcebb3d27",140 "language": "R",141 "lines": 290,142 "truncated": false,143 "block": 10,144 "row": 18820145 },146 {147 "path": "R/parse_longformat_generic.R",148 "sha256": "0548af8a8c8a464a4226fb7769a11003e9608db370b8ebda1319cdb959fc954b",149 "language": "R",150 "lines": 705,151 "truncated": false,152 "block": 10,153 "row": 18928154 },155 {156 "path": "R/parse_maxquant.R",157 "sha256": "e7f9012e2b50a7b6ecc7ee3b9325d1facaa2d5a9d89ce3be77586fa31bb2b38c",158 "language": "R",159 "lines": 323,160 "truncated": false,161 "block": 10,162 "row": 18828163 },164 {165 "path": "R/parse_metamorpheus.R",166 "sha256": "b4d32776b12ac98842537cd2acae46ec5b1e3e503209d69d24a5e0656866e547",167 "language": "R",168 "lines": 153,169 "truncated": false,170 "block": 10,171 "row": 18618172 },173 {174 "path": "R/parse_openms.R",175 "sha256": "419655f4d16cf00d11aea57e298a6bb08ffc9fdc654c250fea218f555b1e4059",176 "language": "R",177 "lines": 250,178 "truncated": false,179 "block": 10,180 "row": 18756181 },182 {183 "path": "R/parse_peaks.R",184 "sha256": "2e4c2b3289ca506fa7d565aa35dfe5919b13ddc7a9291a93d46c0106d9391de0",185 "language": "R",186 "lines": 96,187 "truncated": false,188 "block": 10,189 "row": 18463190 },191 {192 "path": "R/parse_proteomediscoverer_txt.R",193 "sha256": "36b928ca47f69adcf10295a957a260224b950771a77eda18c8cbdf72e531e1d9",194 "language": "R",195 "lines": 270,196 "truncated": false,197 "block": 10,198 "row": 18818199 },200 {201 "path": "R/plot_benchmark.R",202 "sha256": "c184ba7c8ccc766b51becad150373cd73ffc64133228648e9db2887a19487200",203 "language": "R",204 "lines": 222,205 "truncated": false,206 "block": 10,207 "row": 18628208 },209 {210 "path": "R/plot_differential_detect.R",211 "sha256": "28c650f9e9de828bacf58f458f8bcf8aa8edd3193c65440ddb7270bda5ee54d6",212 "language": "R",213 "lines": 45,214 "truncated": false,215 "block": 10,216 "row": 18130217 },218 {219 "path": "R/plot_missing_values.R",220 "sha256": "e18d77fddc208f53a18e1afc91b8a6da023aeba48b2e77fff5a784cbe482f9e6",221 "language": "R",222 "lines": 171,223 "truncated": false,224 "block": 10,225 "row": 18610226 },227 {228 "path": "R/plot_normalization.R",229 "sha256": "c8c5f8c477838e9749d2ec25a287baed288f9fe267ef49ec91ee1441bb570530",230 "language": "R",231 "lines": 507,232 "truncated": false,233 "block": 10,234 "row": 18880235 },236 {237 "path": "R/plot_peptide_data.R",238 "sha256": "ea86afd829df2557ef8160580782d12f97b1db64e3a1ccb0dc1e66709d47532c",239 "language": "R",240 "lines": 796,241 "truncated": false,242 "block": 10,243 "row": 18929244 },245 {246 "path": "R/plot_protein_stats.R",247 "sha256": "f54966ff777697636053c59b630c8633324bdd980a503bd78660bee69bc6d992",248 "language": "R",249 "lines": 184,250 "truncated": false,251 "block": 10,252 "row": 18603253 },254 {255 "path": "R/plot_retention_time.R",256 "sha256": "fc4cb86b9a0e1cc8c24c1f46de3a2a1e94a754c5457a78c83892661c7a5fb2c6",257 "language": "R",258 "lines": 532,259 "truncated": false,260 "block": 10,261 "row": 18906262 },263 {264 "path": "R/plot_sample_metadata.R",265 "sha256": "c4e376d0646053e463fed15b49e58f2e34d7ba5c6090d5fb41475e3c351742e8",266 "language": "R",267 "lines": 428,268 "truncated": false,269 "block": 10,270 "row": 18870271 },272 {273 "path": "R/plot_sample_pca.R",274 "sha256": "dd651de072b2729b8141b5f08bbeae9798512a92454863d78f2f2152cc37fcd9",275 "language": "R",276 "lines": 237,277 "truncated": false,278 "block": 10,279 "row": 18755280 },281 {282 "path": "R/plot_score_distributions.R",283 "sha256": "a52311cf5c3707ed6da0d620d42a74d200bd3ca3909b67d8596e6123f31ec07e",284 "language": "R",285 "lines": 121,286 "truncated": false,287 "block": 10,288 "row": 18390289 },290 {291 "path": "R/plot_variance_explained.R",292 "sha256": "28da8de970d2fcf8b5f7edebc2a35ec8ec25bae7e63029dbcd3b0f2d5cdd67cc",293 "language": "R",294 "lines": 163,295 "truncated": false,296 "block": 10,297 "row": 18633298 },299 {300 "path": "R/plot_volcano.R",301 "sha256": "0f5cc6ddbbd384ff17e8385261454b498534dea865b8900ad3a1b53c0612db27",302 "language": "R",303 "lines": 356,304 "truncated": false,305 "block": 10,306 "row": 18838307 },308 {309 "path": "R/process_peptide_data.R",310 "sha256": "e172d7fa2d96ac92820d5b8eb46a8829c6466049ab302ab95a7e917be6860a45",311 "language": "R",312 "lines": 655,313 "truncated": false,314 "block": 10,315 "row": 18911316 },317 {318 "path": "R/quickstart.R",319 "sha256": "b3aa3cbe1591f0e62943c4a1abb224efd9c96f5e5de3cb541f2cea3cfe1a39c6",320 "language": "R",321 "lines": 293,322 "truncated": false,323 "block": 10,324 "row": 18854325 },326 {327 "path": "R/report_as_rmarkdown.R",328 "sha256": "98d729d3d3fd2f1cf8da6821bb540a3ee460edebb7f80808ecf1f5e0f9b3922d",329 "language": "R",330 "lines": 195,331 "truncated": false,332 "block": 10,333 "row": 18666334 },335 {336 "path": "R/rollup.R",337 "sha256": "1e305c5fdb8fd89b3168ecf0061bd47468e79613fae85ea798d88dd85a22ab22",338 "language": "R",339 "lines": 227,340 "truncated": false,341 "block": 10,342 "row": 18724343 },344 {345 "path": "R/sample_metadata.R",346 "sha256": "c69206ca16b498d3bacd55f1cacdc191a3fa552d8d61b5207a370c1cf652e27c",347 "language": "R",348 "lines": 980,349 "truncated": false,350 "block": 10,351 "row": 18939352 },353 {354 "path": "R/stats_differential_abundance.R",355 "sha256": "dc1e7e79c759f7d6d14ca320e9521219a932a56f1c8a1804013eb508821cf3d8",356 "language": "R",357 "lines": 715,358 "truncated": false,359 "block": 10,360 "row": 18924361 },362 {363 "path": "R/stats_differential_detect.R",364 "sha256": "f243aa066a2b1472646187fbef2febaeec2a76cd3981292fefb57be1b9d50f63",365 "language": "R",366 "lines": 512,367 "truncated": false,368 "block": 10,369 "row": 18877370 },371 {372 "path": "R/stats_summary.R",373 "sha256": "6fd2f04a7f79e655d2f5f49085e0eb3c359b3230ed49a7d20a5c2cbe8c0a57a2",374 "language": "R",375 "lines": 297,376 "truncated": false,377 "block": 10,378 "row": 18810379 },380 {381 "path": "R/util_expressionset.R",382 "sha256": "d3feb12e584dd1579c7d24b175e5a0b6e76eb1a16747bc1769bd18fd8fc7ee41",383 "language": "R",384 "lines": 79,385 "truncated": false,386 "block": 10,387 "row": 18289388 },389 {390 "path": "R/util_fasta.R",391 "sha256": "236396c56496fac51af8f232836a753895bba1317d8d715a7b04f7edbf25247f",392 "language": "R",393 "lines": 178,394 "truncated": false,395 "block": 10,396 "row": 18543397 },398 {399 "path": "R/util_files.R",400 "sha256": "bd814616a49228d3544184df40a7cbbd0c4aa1282ed8d0ad1298f7a6fb2cf5e4",401 "language": "R",402 "lines": 478,403 "truncated": false,404 "block": 10,405 "row": 18858406 },407 {408 "path": "R/util_generic.R",409 "sha256": "0e42670225a68fdde3af23976c3e47231f6e356a009f2e760eb264527a9b52d2",410 "language": "R",411 "lines": 718,412 "truncated": false,413 "block": 10,414 "row": 18868415 },416 {417 "path": "R/util_infer_metadata_from_file.R",418 "sha256": "71eab91c455fb1bc8eb10006e290bc5673f1ae277bf4718be94ffe45bd028d89",419 "language": "R",420 "lines": 294,421 "truncated": false,422 "block": 10,423 "row": 18725424 },425 {426 "path": "R/util_log.R",427 "sha256": "89830ace5c9af2ad2668dda549e84c939b131e7a4312a590607ed926a7a619c3",428 "language": "R",429 "lines": 122,430 "truncated": false,431 "block": 10,432 "row": 18344433 },434 {435 "path": "R/util_normalization.R",436 "sha256": "a073b52fca35b57e2cab48806af97c965d8484b8adb7fec007f6243fb3f8bbb2",437 "language": "R",438 "lines": 320,439 "truncated": false,440 "block": 10,441 "row": 18834442 },443 {444 "path": "R/util_rmarkdown.R",445 "sha256": "70fb0d211034a4843994d1905581b9d8c3fd30b4a952d1f313b0422b8344261b",446 "language": "R",447 "lines": 92,448 "truncated": false,449 "block": 10,450 "row": 18287451 },452 {453 "path": "README.Rmd",454 "sha256": "df537b030b3639c27fd71e58d78c9febea9aea3f178c47f4490d200043302ba7",455 "language": "R",456 "lines": 231,457 "truncated": false,458 "block": 10,459 "row": 18791460 },461 {462 "path": "README.md",463 "sha256": "163856c5da8a7bbb9c5a5188fef4fdaa23c789032a6d9401d02f48d2cc26c650",464 "language": "Text",465 "lines": 277,466 "truncated": false,467 "block": 10,468 "row": 20011469 },470 {471 "path": "doc/custom_limma.Rmd",472 "sha256": "2f876153e8b85c60250596620760f2c638984dab29f98052ac51e208e41ca45e",473 "language": "R",474 "lines": 273,475 "truncated": false,476 "block": 10,477 "row": 18765478 },479 {480 "path": "doc/custom_norm_dea.Rmd",481 "sha256": "c775e67bb578c94854160a66fd0fba8b70a47789dc61d1a404687460b24d426f",482 "language": "R",483 "lines": 209,484 "truncated": false,485 "block": 10,486 "row": 18688487 },488 {489 "path": "doc/differential_detection.Rmd",490 "sha256": "b8ada12c6ea40c6271440ef24d0824c283a2f74478a79a413e66a6d70f78fe36",491 "language": "R",492 "lines": 175,493 "truncated": false,494 "block": 10,495 "row": 18636496 },497 {498 "path": "doc/differential_expression_analysis.Rmd",499 "sha256": "75385b0e12ae1ad25cebd5761c0617ea8aff837df7c85350d1e7d410b6efeee6",500 "language": "R",501 "lines": 104,502 "truncated": false,503 "block": 10,504 "row": 18484505 },506 {507 "path": "doc/docker.Rmd",508 "sha256": "338972726b77f6ba81805800a1a5f97021c09d50346cd7cdc4a878445962530d",509 "language": "R",510 "lines": 230,511 "truncated": false,512 "block": 10,513 "row": 18795514 },515 {516 "path": "doc/intro.Rmd",517 "sha256": "d6fc991f1097d1c8a6c764d018f529c6e4b9574439d7055131dff067b86cda27",518 "language": "R",519 "lines": 322,520 "truncated": false,521 "block": 10,522 "row": 18897523 },524 {525 "path": "doc/rpackage.Rmd",526 "sha256": "95dc23096ca5aa12586ee1d451b19aaecb89e279f7ddac4592e7f76d31dbe4e4",527 "language": "R",528 "lines": 165,529 "truncated": false,530 "block": 10,531 "row": 18506532 },533 {534 "path": "doc/userguide.Rmd",535 "sha256": "ed35997627dfc253bf6d587463c090d6e1a47b0a78c9a24c36f8ae5602fe87d9",536 "language": "R",537 "lines": 478,538 "truncated": false,539 "block": 10,540 "row": 18879541 },542 {543 "path": "docker/msdap_launcher_unix.sh",544 "sha256": "f9b899bd877ffc0f06411087aeaf25af55557565244a443d0f809a61dace0a73",545 "language": "Shell",546 "lines": 83,547 "truncated": false,548 "block": 10,549 "row": 19530550 },551 {552 "path": "examples/example_Klaassen2018_pmid26931375.R",553 "sha256": "edea67f01d194a79008049704a0084881eb1a6be43ed96522083850ffa4ccdd9",554 "language": "R",555 "lines": 51,556 "truncated": false,557 "block": 10,558 "row": 18093559 },560 {561 "path": "examples/example_OConnel2018_pmid29635916.R",562 "sha256": "5a6e14b33f59433686ae5f7dca6a0fb1284cda049d490015a73ebf50c072e7c4",563 "language": "R",564 "lines": 49,565 "truncated": false,566 "block": 10,567 "row": 17985568 },569 {570 "path": "inst/rmd/report.Rmd",571 "sha256": "cd1d74dbb05ca7ba211f0985fc95585f336edb06345e3e696074a648cb44bab3",572 "language": "R",573 "lines": 723,574 "truncated": false,575 "block": 10,576 "row": 18934577 },578 {579 "path": "tests/exploration/msempire_debug_false_negative_results.R",580 "sha256": "125718607003d24b0296ee864207d67cc8e4d50dbb0d06fa054c0e35cda13104",581 "language": "R",582 "lines": 99,583 "truncated": false,584 "block": 10,585 "row": 18337586 },587 {588 "path": "tests/exploration/msempire_feedback.R",589 "sha256": "f71012d2e2a5203f7c23b799158f1d8a6eb51b24195d00834f2b4028a20eb69c",590 "language": "R",591 "lines": 34,592 "truncated": false,593 "block": 10,594 "row": 18026595 },596 {597 "path": "tests/exploration/msempire_reproducibility_needs_set-seed.R",598 "sha256": "4125e201206a85795d1734b89aeee59579ad79edd599804a158bb6e703933721",599 "language": "R",600 "lines": 84,601 "truncated": false,602 "block": 10,603 "row": 18338604 },605 {606 "path": "tests/exploration/msqrob_pvalue_histogram.R",607 "sha256": "4121921870db96e0d3fff9593587995b15911eb3cdf75c41be8c5467b4385ecf",608 "language": "R",609 "lines": 47,610 "truncated": false,611 "block": 10,612 "row": 18075613 },614 {615 "path": "tests/prepare_test_datasets.R",616 "sha256": "8d8fdd48301180a380e3d381625eed888174a94841cb10a66bb67e7e614c751f",617 "language": "R",618 "lines": 72,619 "truncated": false,620 "block": 10,621 "row": 18376622 },623 {624 "path": "tests/testthat.R",625 "sha256": "b7ea1fb4b2b769b8f5665cf1e3d5e8cd2bd475f9fc44a1e4a28bb3d3fe1f6d6e",626 "language": "R",627 "lines": 20,628 "truncated": false,629 "block": 10,630 "row": 17885631 },632 {633 "path": "tests/testthat/helper.R",634 "sha256": "720ed67576ec0bec1ba0701449557a0c5468c1c22e51ee3fac864ac5ff0df02a",635 "language": "R",636 "lines": 4,637 "truncated": false,638 "block": 10,639 "row": 17861640 },641 {642 "path": "tests/testthat/test_dea_reproducibility.R",643 "sha256": "7fc2e2b570ccf1fdeeaacdb651a18c4b5068af7ec39a29bf5c141b7c1abf471f",644 "language": "R",645 "lines": 34,646 "truncated": false,647 "block": 10,648 "row": 17994649 },650 {651 "path": "tests/testthat/test_filtering.R",652 "sha256": "7a6211267aa0875164711c1cbd2885e5868ecf6f6f5708bb840ca2e4a0b7b1c3",653 "language": "R",654 "lines": 52,655 "truncated": false,656 "block": 10,657 "row": 18303658 },659 {660 "path": "tests/testthat/test_fragpipe_parser.R",661 "sha256": "9ec74b8f51c8ef8da350404a1c687e78e161e2bec1f43baa38d8d442d1eeef86",662 "language": "R",663 "lines": 164,664 "truncated": false,665 "block": 10,666 "row": 18719667 },668 {669 "path": "tests/testthat/test_normalization.R",670 "sha256": "d39972b9a7e0c6951e2ca63268a0aca30898643fa2e23d56b0a555aa65a361b8",671 "language": "R",672 "lines": 45,673 "truncated": false,674 "block": 10,675 "row": 18053676 },677 {678 "path": "tests/testthat/test_normalization_reproducibility.R",679 "sha256": "29f09c38c907db6901d27de560440ed3ab8b4be9d9e3d99bac95e2029288bc13",680 "language": "R",681 "lines": 29,682 "truncated": false,683 "block": 10,684 "row": 17952685 },686 {687 "path": "tests/testthat/test_pipeline-vs-msempire.R",688 "sha256": "9556b3bb6febc56e0b560c6fa2f86c94574af0699fa1db0d13975a2d983f73f6",689 "language": "R",690 "lines": 91,691 "truncated": false,692 "block": 10,693 "row": 18404694 },695 {696 "path": "tests/testthat/test_pipeline-vs-msqrob.R",697 "sha256": "509ccc20a585151ac2205abcc22503c070b662ca6ccbb58addd12ba35c3d5a06",698 "language": "R",699 "lines": 234,700 "truncated": false,701 "block": 10,702 "row": 18734703 }704 ]705}