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__broadinstitute__cellbender.json489 linesDownload Raw Back to 7e
1{2 "format": "oscr-script-manifest/1",3 "repository": "github.com/broadinstitute/cellbender",4 "url": "https://github.com/broadinstitute/CellBender/",5 "host": "github.com",6 "commit": "f36ae299d565baccf20f015ceb10a6d6a3ea3006",7 "license": "BSD-3-Clause",8 "license_confirmed_by": "license file LICENSE",9 "redistribution": "yes",10 "files": [11  {12   "path": "LICENSE",13   "sha256": "bb9ca6c7a9512961a8dc45829c849bb6e4d8546b7fbbe88a59387b6ae32011d0",14   "language": "License",15   "lines": 26,16   "truncated": false,17   "block": 6,18   "row": 196119  },20  {21   "path": "README.rst",22   "sha256": "d3936cdd3c1a738408c4d6ae0d0bd1e9e57d2b484463f13ebfe7b2357be19eb2",23   "language": "Text",24   "lines": 162,25   "truncated": false,26   "block": 8,27   "row": 1044228  },29  {30   "path": "benchmarking/cellbender_benchmarking.ipynb",31   "sha256": "1735f3fcea9eac8b48a556457b80494a217bb8cf7b64c5a8609c9471912fea33",32   "language": "Jupyter",33   "lines": 1893,34   "truncated": false,35   "block": 6,36   "row": 123037  },38  {39   "path": "benchmarking/run_notebook.py",40   "sha256": "c0d5b51a1debdfcf64b6c5fde652ef5a7680b5b2c2beb94573633ecf32a4b9a5",41   "language": "Python",42   "lines": 39,43   "truncated": false,44   "block": 6,45   "row": 2657646  },47  {48   "path": "benchmarking/submit_benchmarks.py",49   "sha256": "d1662a1de0f3e9d6a2965332f8e4abda038bfc0acdbc75d0ca98e29250b8ebd9",50   "language": "Python",51   "lines": 360,52   "truncated": false,53   "block": 7,54   "row": 449655  },56  {57   "path": "benchmarking/submit_single.py",58   "sha256": "f227f5af691639f6ffc64774686d1040f8a5fe76ccfa5fac891ae2625d974e4e",59   "language": "Python",60   "lines": 143,61   "truncated": false,62   "block": 6,63   "row": 4042864  },65  {66   "path": "build_docker_local.sh",67   "sha256": "690a2fb3c11a2c6818c98a81314cb8b3b26517d99c5b34f53fe2960c9b57d073",68   "language": "Shell",69   "lines": 8,70   "truncated": false,71   "block": 8,72   "row": 660573  },74  {75   "path": "build_docker_release.sh",76   "sha256": "00cc51a79c30a3ccefa4a902590f3b2b2c8d78c44cb003e48b4e6be4a436511a",77   "language": "Shell",78   "lines": 10,79   "truncated": false,80   "block": 8,81   "row": 660882  },83  {84   "path": "cellbender/__init__.py",85   "sha256": "cd599bcca89997abd772455f5c64b657ae7d4236b565ae1d6488f69af01ee310",86   "language": "Python",87   "lines": 24,88   "truncated": false,89   "block": 6,90   "row": 2463091  },92  {93   "path": "cellbender/base_cli.py",94   "sha256": "e060b51a07f7f43aada04b06487f7f1efb36849ddb0dd949c87c808df59f10d1",95   "language": "Python",96   "lines": 122,97   "truncated": false,98   "block": 6,99   "row": 37465100  },101  {102   "path": "cellbender/monitor.py",103   "sha256": "9a7f609b95784509588f40e35b874860794afca3033e7913331747967897eb6f",104   "language": "Python",105   "lines": 46,106   "truncated": false,107   "block": 6,108   "row": 29846109  },110  {111   "path": "cellbender/remove_background/argparser.py",112   "sha256": "324611ed4072c2c06c3b9dc5f5932c22507e6d05de5b172cdde71a446595c58e",113   "language": "Python",114   "lines": 394,115   "truncated": false,116   "block": 7,117   "row": 6243118  },119  {120   "path": "cellbender/remove_background/checkpoint.py",121   "sha256": "0e4704f99652a3013c74c97e0ac59390bf3753781125f80310ce796b4199383f",122   "language": "Python",123   "lines": 423,124   "truncated": false,125   "block": 7,126   "row": 7081127  },128  {129   "path": "cellbender/remove_background/cli.py",130   "sha256": "9395a83b65747335603f77ba40c0422c1cabf8df672b17df91bdde8123d3805c",131   "language": "Python",132   "lines": 241,133   "truncated": false,134   "block": 7,135   "row": 3033136  },137  {138   "path": "cellbender/remove_background/consts.py",139   "sha256": "49ef5b9ab312485d98cf0bd5fe8cf2c891f334919a2a1c71de15148b64e04643",140   "language": "Python",141   "lines": 116,142   "truncated": false,143   "block": 6,144   "row": 38279145  },146  {147   "path": "cellbender/remove_background/data/dataprep.py",148   "sha256": "baccd5347e95ce23303d318c221e4fd6294247b478c8a35655259ce707618955",149   "language": "Python",150   "lines": 292,151   "truncated": false,152   "block": 7,153   "row": 4384154  },155  {156   "path": "cellbender/remove_background/data/dataset.py",157   "sha256": "0b9865cd27e4221bab969066469b3ad60411624caeecfc1e03a169e9860c3fa4",158   "language": "Python",159   "lines": 547,160   "truncated": false,161   "block": 7,162   "row": 10007163  },164  {165   "path": "cellbender/remove_background/data/extras/simulate.py",166   "sha256": "6fb04e7b6ac16efea14a646281572faf077a457cac3bdd2df708a69dd5c20d1e",167   "language": "Python",168   "lines": 922,169   "truncated": false,170   "block": 7,171   "row": 11549172  },173  {174   "path": "cellbender/remove_background/data/io.py",175   "sha256": "377ec9c165537e0052778a8dc7bee5f55febbb2ef8acb08d1673b4d786e9aaf7",176   "language": "Python",177   "lines": 1210,178   "truncated": false,179   "block": 8,180   "row": 405181  },182  {183   "path": "cellbender/remove_background/data/priors.py",184   "sha256": "b06015e9cd3d0af4be74efa13a64a4d8e038ac7c3c3d586a61bd66135665e4c4",185   "language": "Python",186   "lines": 391,187   "truncated": false,188   "block": 7,189   "row": 6962190  },191  {192   "path": "cellbender/remove_background/distributions/NegativeBinomialPoissonConv.py",193   "sha256": "898afe3bf533abd8bdf9a89bbb9e2a9b9f9f05865c1ffc934360ededcb816689",194   "language": "Python",195   "lines": 162,196   "truncated": false,197   "block": 6,198   "row": 44769199  },200  {201   "path": "cellbender/remove_background/distributions/NegativeBinomialPoissonConvApprox.py",202   "sha256": "dcd07eb915d38753c0d467e534add68cd74e3f746e33481672bab92de010f31b",203   "language": "Python",204   "lines": 153,205   "truncated": false,206   "block": 6,207   "row": 43322208  },209  {210   "path": "cellbender/remove_background/distributions/NullDist.py",211   "sha256": "d634e38cbfd78f22af73d7ae139eaecbba557e278c618ce48a38ed1ca864856a",212   "language": "Python",213   "lines": 63,214   "truncated": false,215   "block": 6,216   "row": 33922217  },218  {219   "path": "cellbender/remove_background/downstream.py",220   "sha256": "f1d3e74acd7fe79d9263ecb350088ba34bd6441c49116d07ad5a512ed386312c",221   "language": "Python",222   "lines": 487,223   "truncated": false,224   "block": 7,225   "row": 9017226  },227  {228   "path": "cellbender/remove_background/estimation.py",229   "sha256": "c0f4b67bf5694bdd0d1b77bff4cd8d48899b76060ef410cbad2e66f50c013424",230   "language": "Python",231   "lines": 864,232   "truncated": false,233   "block": 7,234   "row": 11332235  },236  {237   "path": "cellbender/remove_background/exceptions.py",238   "sha256": "cd929c4ce77ec71cf068fec1f608fb7bb5a294fa9164507517dd32e24eb68f2a",239   "language": "Python",240   "lines": 24,241   "truncated": false,242   "block": 6,243   "row": 23390244  },245  {246   "path": "cellbender/remove_background/model.py",247   "sha256": "7bbaf0cf9d764d394fb58fe31fe2f53a4be62c1937b66202b1ca9c573ee9cbad",248   "language": "Python",249   "lines": 638,250   "truncated": false,251   "block": 7,252   "row": 10161253  },254  {255   "path": "cellbender/remove_background/posterior.py",256   "sha256": "97656608b7df8b67eeda2de1b45a2d123c206b0c27fd6b696303c234da644888",257   "language": "Python",258   "lines": 1768,259   "truncated": false,260   "block": 8,261   "row": 806262  },263  {264   "path": "cellbender/remove_background/report.ipynb",265   "sha256": "f0d7243d1506dfe8d51c9dc1ddc1a65ca66f8dace077ccd79141decaa3110ab0",266   "language": "Jupyter",267   "lines": 54,268   "truncated": false,269   "block": 5,270   "row": 16219271  },272  {273   "path": "cellbender/remove_background/report.py",274   "sha256": "71adc65b2ac0e19a3372bb54cfa7266457bc965b5d7189bee378e93eb0c47b90",275   "language": "Python",276   "lines": 2045,277   "truncated": false,278   "block": 8,279   "row": 880280  },281  {282   "path": "cellbender/remove_background/run.py",283   "sha256": "0f7255b3ccdcde11d5cd99ad857897e8b92d7d2f6d24249006a128c98aea0ead",284   "language": "Python",285   "lines": 856,286   "truncated": false,287   "block": 7,288   "row": 11235289  },290  {291   "path": "cellbender/remove_background/sparse_utils.py",292   "sha256": "6245da862ba6f740881692927999b47e0aef687e50cb9222cfb44267c86958b9",293   "language": "Python",294   "lines": 100,295   "truncated": false,296   "block": 6,297   "row": 37006298  },299  {300   "path": "cellbender/remove_background/train.py",301   "sha256": "73a984c1ed9a4597cdc2547ccb512fd99bce9f5e78383d5428eff6c350b297a4",302   "language": "Python",303   "lines": 300,304   "truncated": false,305   "block": 7,306   "row": 5207307  },308  {309   "path": "cellbender/remove_background/vae/base.py",310   "sha256": "17e682451f2fbc308b08d9bba1ddfb273a2c07845fad20b8c1087919f6853d1a",311   "language": "Python",312   "lines": 148,313   "truncated": false,314   "block": 6,315   "row": 42958316  },317  {318   "path": "cellbender/remove_background/vae/decoder.py",319   "sha256": "b3e21deae04b95c1118b049d7fa15262291278f2714bbaa0263f515ce9446d13",320   "language": "Python",321   "lines": 47,322   "truncated": false,323   "block": 6,324   "row": 32050325  },326  {327   "path": "cellbender/remove_background/vae/encoder.py",328   "sha256": "dd6decb76feda6a1d0d187feb4b51f5656befdc8b45f731240b5783f67f4786d",329   "language": "Python",330   "lines": 381,331   "truncated": false,332   "block": 7,333   "row": 6626334  },335  {336   "path": "docs/source/conf.py",337   "sha256": "5e89c59de19d6da0749c3212f5ab7cfa8befe8cbe0932907cd2c11a73e1c3768",338   "language": "Python",339   "lines": 72,340   "truncated": false,341   "block": 6,342   "row": 33879343  },344  {345   "path": "examples/remove_background/generate_tiny_10x_dataset.py",346   "sha256": "0600c89a5afffd06f374edfafa2363a747689bc27cd5112bf2d7b4a426ec251f",347   "language": "Python",348   "lines": 85,349   "truncated": false,350   "block": 6,351   "row": 36003352  },353  {354   "path": "tests/conftest.py",355   "sha256": "06540485784e7bacfd4c1ddcf3ac21212c8fbbff2b9efb7da94c8a0b89db324d",356   "language": "Python",357   "lines": 235,358   "truncated": false,359   "block": 7,360   "row": 628361  },362  {363   "path": "tests/mckp_memory_profiling.py",364   "sha256": "58bbed8ffe51513a33e40c5074bbf82df3ff0e7141f5ee427ab3f1f804f751e9",365   "language": "Python",366   "lines": 144,367   "truncated": false,368   "block": 6,369   "row": 42314370  },371  {372   "path": "tests/miniwdl_check_wdl.sh",373   "sha256": "bb81fcbfe78b3b5235e11a05c088b66f2564f4d0bb18b77dbe48d7ddd03e3a38",374   "language": "Shell",375   "lines": 13,376   "truncated": false,377   "block": 8,378   "row": 6663379  },380  {381   "path": "tests/test_checkpoint.py",382   "sha256": "a0228911384c43b963a5a97c797398c1459ffd0eab4b1c0f700b1a76ac7a58cc",383   "language": "Python",384   "lines": 614,385   "truncated": false,386   "block": 7,387   "row": 9737388  },389  {390   "path": "tests/test_dataprep.py",391   "sha256": "0ea57f78bebd5a5ca89c834f8848e2c1a833e97dfb1c08d8527c429f9b714b26",392   "language": "Python",393   "lines": 97,394   "truncated": false,395   "block": 6,396   "row": 36050397  },398  {399   "path": "tests/test_dataset.py",400   "sha256": "9bbb13bf570f8768d9c533acffd40a2e40a67be7b8974ed1dc21fc473611c3cf",401   "language": "Python",402   "lines": 36,403   "truncated": false,404   "block": 6,405   "row": 23402406  },407  {408   "path": "tests/test_downstream.py",409   "sha256": "1ec80d6439fb36d9353d2443e0f2e7726a60a7850d4cf99b60c947b987770c10",410   "language": "Python",411   "lines": 122,412   "truncated": false,413   "block": 6,414   "row": 40571415  },416  {417   "path": "tests/test_estimation.py",418   "sha256": "f18b5fb3dbe2e4cecb6df11a82e29b0fe2d5afb41588311501fe2890367cd73b",419   "language": "Python",420   "lines": 410,421   "truncated": false,422   "block": 7,423   "row": 6420424  },425  {426   "path": "tests/test_infer.py",427   "sha256": "c87a05499b27b9a3e1e4285673b15b21c97cc076bdb7f9e9f5ba83954bd5c034",428   "language": "Python",429   "lines": 301,430   "truncated": false,431   "block": 7,432   "row": 4450433  },434  {435   "path": "tests/test_integration.py",436   "sha256": "d933de162654503b8528daa7c191c2735fb0567b82be356d46b4e558cd114f65",437   "language": "Python",438   "lines": 65,439   "truncated": false,440   "block": 6,441   "row": 33615442  },443  {444   "path": "tests/test_io.py",445   "sha256": "0fb7e3883c9078d25b65629730872527d2ee28b468f153c2c27145b41de5f957",446   "language": "Python",447   "lines": 218,448   "truncated": false,449   "block": 6,450   "row": 45562451  },452  {453   "path": "tests/test_monitor.py",454   "sha256": "9ab5e8be8ca68a890d28b1190fbc44567025b107a5867df4b3e2fa883e7cb973",455   "language": "Python",456   "lines": 21,457   "truncated": false,458   "block": 6,459   "row": 23059460  },461  {462   "path": "tests/test_posterior.py",463   "sha256": "4927b1cc11f4588e70ee0a9324c4fbe1f5e57b55b91e60522ca0c2a96bcb4cef",464   "language": "Python",465   "lines": 445,466   "truncated": false,467   "block": 7,468   "row": 7372469  },470  {471   "path": "tests/test_sparse_utils.py",472   "sha256": "239ce0bc6038096765e2d4b74131ba9b861f98405ec68e9b244101d23a4783b2",473   "language": "Python",474   "lines": 200,475   "truncated": false,476   "block": 6,477   "row": 43560478  },479  {480   "path": "tests/test_train.py",481   "sha256": "ec0e9c1a810f51d546679e21f19b982c2bb0e8d034e8f9a0f7b926d06ede0795",482   "language": "Python",483   "lines": 133,484   "truncated": false,485   "block": 6,486   "row": 40316487  }488 ]489}