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__openomics__cell-seek.json318 linesDownload Raw Back to 6d
1{2 "format": "oscr-script-manifest/1",3 "repository": "github.com/openomics/cell-seek",4 "url": "https://github.com/OpenOmics/cell-seek",5 "host": "github.com",6 "commit": "0f54b5b57566dcd23f1a98dcf845bf6e0a7391fb",7 "license": "MIT",8 "license_confirmed_by": "license file LICENSE",9 "redistribution": "yes",10 "files": [11  {12   "path": "LICENSE",13   "sha256": "c4b274d22d66e950ab110dcb70108508fe49ec3002703618c2bea67a2ba33f39",14   "language": "License",15   "lines": 21,16   "truncated": false,17   "block": 11,18   "row": 1398219  },20  {21   "path": "README.md",22   "sha256": "91abc6ac132c9fdb29149aae41db255d475bf6f82b1f1618bdd4d42cbdde300d",23   "language": "Text",24   "lines": 89,25   "truncated": false,26   "block": 13,27   "row": 676928  },29  {30   "path": "docker/ShinyCell2/build_shinycell.R",31   "sha256": "1f0581ca17c47448e632ce4ca63a0a71336c9a6a9101776e8a3ad8eddebf4a52",32   "language": "R",33   "lines": 554,34   "truncated": false,35   "block": 13,36   "row": 310837  },38  {39   "path": "docker/ShinyCell2/git_installs.sh",40   "sha256": "50777fbb857797ffece6f3629123d3724529fcfc01c91516af8d900876a823eb",41   "language": "Shell",42   "lines": 15,43   "truncated": false,44   "block": 13,45   "row": 434546  },47  {48   "path": "docker/ShinyCell2/ingest_10x.R",49   "sha256": "96a14f6a8914cbc0bc21d0ce8ac6399e2c0c43d8a56d026125e4d2099e8f3f70",50   "language": "R",51   "lines": 289,52   "truncated": false,53   "block": 13,54   "row": 270855  },56  {57   "path": "docker/ShinyCell2/install_packages.R",58   "sha256": "39426d34c5eda6aa9f011c7112aebde904f19c68972d910b0308579eee4557ff",59   "language": "R",60   "lines": 76,61   "truncated": false,62   "block": 13,63   "row": 124564  },65  {66   "path": "docker/ShinyCell2/seurat_inspector.R",67   "sha256": "9166665c615efea8bec1e1b774ac9fc4ee342b0d6b715147832dd11a51db8083",68   "language": "R",69   "lines": 525,70   "truncated": false,71   "block": 13,72   "row": 304173  },74  {75   "path": "docker/sc_atac_analysis/signacMultiSampleQC.R",76   "sha256": "cff23306ea9986b82d972b3914757b3eb85d854ac644afcb2a6998253d459d4e",77   "language": "R",78   "lines": 1294,79   "truncated": false,80   "block": 13,81   "row": 330982  },83  {84   "path": "docker/sc_atac_analysis/signacMultiSampleQCreport.Rmd",85   "sha256": "4c86deb21e6740a54844dbf1b8dd1604bc4cde153f0a9146556be85c555c28d0",86   "language": "R",87   "lines": 307,88   "truncated": false,89   "block": 13,90   "row": 289691  },92  {93   "path": "docker/sc_atac_analysis/signacSampleQC.R",94   "sha256": "4f867553747ffbba08538e22e500d366ad660976013d48d6bd2d18ff5011b6a7",95   "language": "R",96   "lines": 921,97   "truncated": false,98   "block": 13,99   "row": 3185100  },101  {102   "path": "docker/sc_atac_analysis/signacSampleQCReport.Rmd",103   "sha256": "9bf35edb1ebb4ae26fbb4a8d436ec5096eb2c20e138b70bd9675f1de75e4acf5",104   "language": "R",105   "lines": 280,106   "truncated": false,107   "block": 13,108   "row": 2780109  },110  {111   "path": "src/__init__.py",112   "sha256": "5db2f3d8163e1f914cf13ce940d8d69e346dcdcec6b08722a9381c148fec9bc5",113   "language": "Python",114   "lines": 16,115   "truncated": false,116   "block": 12,117   "row": 4940118  },119  {120   "path": "src/run.py",121   "sha256": "d5ce25f78d04bf8a2824114ea3be230d737deacaf25adbc96dcfb7bb55e09276",122   "language": "Python",123   "lines": 1492,124   "truncated": false,125   "block": 13,126   "row": 394127  },128  {129   "path": "src/run.sh",130   "sha256": "3d00ae3b081c5a571e144088b03c52e4f4a7b094bdfcb4ec97ee24bbb872bbb1",131   "language": "Shell",132   "lines": 291,133   "truncated": false,134   "block": 13,135   "row": 5868136  },137  {138   "path": "src/shells.py",139   "sha256": "5156910f8dff11cdd11eb797fff7c8835cd7bf0bad5d874f1df15d14cc60370b",140   "language": "Python",141   "lines": 70,142   "truncated": false,143   "block": 12,144   "row": 8983145  },146  {147   "path": "src/utils.py",148   "sha256": "9154c30470970deb7572ef96ed0f1eb0b9257e83cc090d55e6159a596e1b0d5f",149   "language": "Python",150   "lines": 367,151   "truncated": false,152   "block": 12,153   "row": 19044154  },155  {156   "path": "workflow/scripts/cellFilterSummary.R",157   "sha256": "5e72c3d3d245ff7f9fdaab5aac0b795cdcc95a7969e62b1d6fe77297082674a2",158   "language": "R",159   "lines": 36,160   "truncated": false,161   "block": 13,162   "row": 1212163  },164  {165   "path": "workflow/scripts/common.py",166   "sha256": "eb35037e8b0f8aa2a494144585931a9a3caa3a3886be339805164219d9c9b02a",167   "language": "Python",168   "lines": 204,169   "truncated": false,170   "block": 12,171   "row": 16540172  },173  {174   "path": "workflow/scripts/create_library_files.py",175   "sha256": "35743fae046b9f22e6f02c7bfb4c76ca4a598cddc3a0bfbf18ed264bf0eeb1e0",176   "language": "Python",177   "lines": 68,178   "truncated": false,179   "block": 12,180   "row": 11017181  },182  {183   "path": "workflow/scripts/generateAggregateCSV_GEX.py",184   "sha256": "7ce317ae27c9201f1a8dfed989f00f2adb89c523dca4214f93649939e584dd08",185   "language": "Python",186   "lines": 16,187   "truncated": false,188   "block": 12,189   "row": 4278190  },191  {192   "path": "workflow/scripts/generateSummaryFiles.py",193   "sha256": "37b2e777b52ce6c08bc71ab94a7058ded6e39cf5935a48f31997e24e0bcee32b",194   "language": "Python",195   "lines": 113,196   "truncated": false,197   "block": 12,198   "row": 12007199  },200  {201   "path": "workflow/scripts/generateSummaryFiles_ATAC.py",202   "sha256": "5727cca8829d0ec2712a1e5777620a511dd13479088711d71e9b56d88cc2faa3",203   "language": "Python",204   "lines": 109,205   "truncated": false,206   "block": 12,207   "row": 11512208  },209  {210   "path": "workflow/scripts/generateSummaryFiles_MULTI.py",211   "sha256": "52e99f832970a4c86fdb40c7439c779341aeeebe4380737b8ffc19d516b4599e",212   "language": "Python",213   "lines": 177,214   "truncated": false,215   "block": 12,216   "row": 15965217  },218  {219   "path": "workflow/scripts/generateSummaryFiles_MULTIOME.py",220   "sha256": "e12834befae412e8455fab9791f97a60395d6997217d38ba8ebe190f7b268a14",221   "language": "Python",222   "lines": 100,223   "truncated": false,224   "block": 12,225   "row": 10219226  },227  {228   "path": "workflow/scripts/seuratCiteSampleQC.R",229   "sha256": "70581444442e2fc3efdc671c0924957804d341c71817d8ddf0157ce9b88d24f8",230   "language": "R",231   "lines": 504,232   "truncated": false,233   "block": 13,234   "row": 3205235  },236  {237   "path": "workflow/scripts/seuratCiteSampleQCReport.Rmd",238   "sha256": "b4dd55b74ba7f5bdab62ddb0ed57d3490c5ed5d177ccb7de2a7c7390553ddd13",239   "language": "R",240   "lines": 365,241   "truncated": false,242   "block": 13,243   "row": 2963244  },245  {246   "path": "workflow/scripts/seuratCiteSampleQCSummaryReport.Rmd",247   "sha256": "3f3d0544621dced7b209a85266eed189a2a173e919a4a11abf0bf4d6106300f0",248   "language": "R",249   "lines": 240,250   "truncated": false,251   "block": 13,252   "row": 2877253  },254  {255   "path": "workflow/scripts/seuratIntegrate.R",256   "sha256": "3ec379f1933cf5e2e10d41498df1b1b98ae324cd8a4d9eb185fd42e785621f25",257   "language": "R",258   "lines": 103,259   "truncated": false,260   "block": 13,261   "row": 2081262  },263  {264   "path": "workflow/scripts/seuratIntegrateSummaryReport.Rmd",265   "sha256": "df3f11204f22ab5348730558597c52e534a8af9d90e554c6575dc2567e69669d",266   "language": "R",267   "lines": 114,268   "truncated": false,269   "block": 13,270   "row": 1757271  },272  {273   "path": "workflow/scripts/seuratSampleQC.R",274   "sha256": "8241a31bd913ec2b3d287be5ed6a1c3dca2ba9140bad3e77f510cb6a98476740",275   "language": "R",276   "lines": 276,277   "truncated": false,278   "block": 13,279   "row": 2901280  },281  {282   "path": "workflow/scripts/seuratSampleQCReport.Rmd",283   "sha256": "5c70e7c771bad2e6045c3f1837391a56011cd7bdc2da202d651eebbd1ac37e16",284   "language": "R",285   "lines": 272,286   "truncated": false,287   "block": 13,288   "row": 2764289  },290  {291   "path": "workflow/scripts/seuratSampleQCSummaryReport.Rmd",292   "sha256": "4656805f102ff4f6358d39913850b8017caf5aa9a2274be1a36e127d94949b29",293   "language": "R",294   "lines": 184,295   "truncated": false,296   "block": 13,297   "row": 2631298  },299  {300   "path": "workflow/scripts/utils.sh",301   "sha256": "90713e79ed60616093dd7ee194514282a81f3054772e3e5bb0c5750076ffc797",302   "language": "Shell",303   "lines": 38,304   "truncated": false,305   "block": 13,306   "row": 4998307  },308  {309   "path": "workflow/scripts/write_multiconfig.py",310   "sha256": "4e995dc749f7d7481475d4d4faef8bab0c1e74a67f769a2db92ec5c2f0d00e7d",311   "language": "Python",312   "lines": 168,313   "truncated": false,314   "block": 12,315   "row": 16902316  }317 ]318}