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
rootmanifests45github.com__huangyh09__brie.json
github.com__huangyh09__brie.json507 linesDownload Raw Back to 45
1{2 "format": "oscr-script-manifest/1",3 "repository": "github.com/huangyh09/brie",4 "url": "https://github.com/huangyh09/brie",5 "host": "github.com",6 "commit": "a9c8d558dfcf593f3a324c783b0c10e866ba3ba5",7 "license": "Apache-2.0",8 "license_confirmed_by": "license file LICENSE",9 "redistribution": "yes",10 "files": [11  {12   "path": "LICENSE",13   "sha256": "6cc530954c3d62d4a5a570cef8cd73be804d4a7630892ce97546d9595615cfa1",14   "language": "License",15   "lines": 204,16   "truncated": false,17   "block": 20,18   "row": 885919  },20  {21   "path": "README.rst",22   "sha256": "2241f3660fa1f87ece7a3e6c150758c0d9ae5f99a90d585c1eeb5d9035cce742",23   "language": "Text",24   "lines": 113,25   "truncated": false,26   "block": 21,27   "row": 311228  },29  {30   "path": "brie/__init__.py",31   "sha256": "e4a7f9e6b8d760889040dfc15b5a510713990a0e8c721ac85fae60c567f4f453",32   "language": "Python",33   "lines": 29,34   "truncated": false,35   "block": 20,36   "row": 1375137  },38  {39   "path": "brie/_cli/__init__.py",40   "sha256": "7f6777ff1f1b3ef8b0aae773d2efcf0644fe158a2be951bf07ea3c1537f10d53",41   "language": "Python",42   "lines": 3,43   "truncated": false,44   "block": 20,45   "row": 1223746  },47  {48   "path": "brie/_cli/_cli.py",49   "sha256": "af83da1fd913b25de4deaacadeb123efcac9ac7783adab58353639f04dc3fce6",50   "language": "Python",51   "lines": 39,52   "truncated": false,53   "block": 20,54   "row": 1415255  },56  {57   "path": "brie/_cli/count.py",58   "sha256": "97c26e61342c90fc3d11d38120e4455a2b3caa4eb7195a25a6641c3af66d211b",59   "language": "Python",60   "lines": 32,61   "truncated": false,62   "block": 20,63   "row": 1473564  },65  {66   "path": "brie/_cli/download.py",67   "sha256": "5b5620b863d619a2638a6ffc56dfbe49d47425470333e7e10aaa952f3896d458",68   "language": "Python",69   "lines": 18,70   "truncated": false,71   "block": 20,72   "row": 1331473  },74  {75   "path": "brie/_cli/extract.py",76   "sha256": "5e443a4e5b40a42cdb723c46ada3010f3f120aee93d0397a5fb952d94c9708e3",77   "language": "Python",78   "lines": 15,79   "truncated": false,80   "block": 20,81   "row": 1316182  },83  {84   "path": "brie/_cli/quant.py",85   "sha256": "56f7bb7c62bc0c32a775f33562c76273b865b28f92f67b6df0f4fed3eff4fd86",86   "language": "Python",87   "lines": 19,88   "truncated": false,89   "block": 20,90   "row": 1334791  },92  {93   "path": "brie/bin/__init__.py",94   "sha256": "7bb154bac2ea39a611524e172196132714986cece6317637e8f1d377ba20d32b",95   "language": "Python",96   "lines": 4,97   "truncated": false,98   "block": 20,99   "row": 12339100  },101  {102   "path": "brie/bin/brie_main.py",103   "sha256": "741215e0b8925f2e77654c6d5f06ac6b8fe9647bc476ca96cd7b817942b55ef4",104   "language": "Python",105   "lines": 13,106   "truncated": false,107   "block": 20,108   "row": 13085109  },110  {111   "path": "brie/bin/count.py",112   "sha256": "d2194ae90a973ceb708b69020730284b5359bb7832a011834b04aae59f666458",113   "language": "Python",114   "lines": 325,115   "truncated": false,116   "block": 20,117   "row": 20735118  },119  {120   "path": "brie/bin/quant.py",121   "sha256": "98f8c98d5a6759e9db76ace187c57663dbad4294fa759dec8ff19fe930a630eb",122   "language": "Python",123   "lines": 223,124   "truncated": false,125   "block": 20,126   "row": 19972127  },128  {129   "path": "brie/models/__init__.py",130   "sha256": "d882d53b54a6b2c66ae575384258a5ea02f2e1b20aeb135a6c2bc10fa7190e89",131   "language": "Python",132   "lines": 4,133   "truncated": false,134   "block": 20,135   "row": 12530136  },137  {138   "path": "brie/models/base_model.py",139   "sha256": "ffa0e05b51370919960d126780976e2f2ee3c114b008e9e8a3ea3cf54341573d",140   "language": "Python",141   "lines": 55,142   "truncated": false,143   "block": 20,144   "row": 14954145  },146  {147   "path": "brie/models/hypothesis_tests.py",148   "sha256": "d7058a17e8b73521e0c56d28c73f703846d0b87391b952bbe6494ba6c5113ba7",149   "language": "Python",150   "lines": 92,151   "truncated": false,152   "block": 20,153   "row": 17030154  },155  {156   "path": "brie/models/model_Beta.py",157   "sha256": "fbbec3aa4dddbbefb20cf2e55766b01e534a8de1bf63e9940176891305a12627",158   "language": "Python",159   "lines": 225,160   "truncated": false,161   "block": 20,162   "row": 19581163  },164  {165   "path": "brie/models/model_TFProb.py",166   "sha256": "ca7f70bb0ef60f8d24e2f8ed76c3b563ef123cc0fdb5174b2ff2d6c28022be42",167   "language": "Python",168   "lines": 273,169   "truncated": false,170   "block": 20,171   "row": 20237172  },173  {174   "path": "brie/models/model_TFProb_dev.py",175   "sha256": "e02a337ed7fb0e7577996dcdf453f96dafdf1354fb2986a83ac8c914d98eba2c",176   "language": "Python",177   "lines": 255,178   "truncated": false,179   "block": 20,180   "row": 20065181  },182  {183   "path": "brie/models/model_wrap.py",184   "sha256": "81caed2b57dd7a5c18507e9dbb2184c2b44888e23b8971b43dbf2698b413cdf1",185   "language": "Python",186   "lines": 314,187   "truncated": false,188   "block": 20,189   "row": 20518190  },191  {192   "path": "brie/models/simulator.py",193   "sha256": "54cb91a8129ff875f3b637e2a2d7b9e3f837a512b11fda2fcc6379e4ad035136",194   "language": "Python",195   "lines": 76,196   "truncated": false,197   "block": 20,198   "row": 16509199  },200  {201   "path": "brie/models/tools.py",202   "sha256": "5f51663837034d7672b761ab27ae4ce0733298e993aa130f3273e6825cdb3d72",203   "language": "Python",204   "lines": 4,205   "truncated": false,206   "block": 20,207   "row": 12345208  },209  {210   "path": "brie/plot/LRtest_plot.py",211   "sha256": "d45e9d8fe08388ce8489954151760fc6c90959630bde21d22e77faf2380a52a6",212   "language": "Python",213   "lines": 134,214   "truncated": false,215   "block": 20,216   "row": 17742217  },218  {219   "path": "brie/plot/__init__.py",220   "sha256": "3af62091e6a37d51ee470ff61c29011ed55776914cd1711239b7667ba07caab1",221   "language": "Python",222   "lines": 2,223   "truncated": false,224   "block": 20,225   "row": 12261226  },227  {228   "path": "brie/plot/base_plot.py",229   "sha256": "70d43402fc67acda18b0eede835142783d60e9f4dcc5891d49ffdb142ca595c6",230   "language": "Python",231   "lines": 117,232   "truncated": false,233   "block": 20,234   "row": 17501235  },236  {237   "path": "brie/settings.py",238   "sha256": "90f9a2d76ed09718d6fea84d72281e3f2809449ab9baea0a1c26ce82822badf4",239   "language": "Python",240   "lines": 6,241   "truncated": false,242   "block": 20,243   "row": 12324244  },245  {246   "path": "brie/utils/__init__.py",247   "sha256": "6a889d958d1e04cc03e21be9dd4743cb52637b7d0259f0938fddfd9a180438c9",248   "language": "Python",249   "lines": 6,250   "truncated": false,251   "block": 20,252   "row": 12689253  },254  {255   "path": "brie/utils/base_utils.py",256   "sha256": "b604965b823adc1d1ed10a5a55e7fb7f4962e3b4a8987c59fea106604e74c0cd",257   "language": "Python",258   "lines": 59,259   "truncated": false,260   "block": 20,261   "row": 15289262  },263  {264   "path": "brie/utils/bias_utils.py",265   "sha256": "d5c6c8b38563638a8346c878a238a95afd0f02f4563aafed35f83b552d6630d0",266   "language": "Python",267   "lines": 344,268   "truncated": false,269   "block": 20,270   "row": 21158271  },272  {273   "path": "brie/utils/count.py",274   "sha256": "206d3f3d92fcb241d9706db97f3b31b47461ad782eac2e614c7670a31f6689eb",275   "language": "Python",276   "lines": 291,277   "truncated": false,278   "block": 20,279   "row": 20270280  },281  {282   "path": "brie/utils/count_droplet.py",283   "sha256": "761a1feda80bca9bbbfcbbc052bb539078a5b08d1da4bd4ebf6d83bf9b267418",284   "language": "Python",285   "lines": 252,286   "truncated": false,287   "block": 20,288   "row": 19973289  },290  {291   "path": "brie/utils/fasta_utils.py",292   "sha256": "e53525e411e49fa6899c8c1cb0636fb9107d62204ac22de2f39cab36dd148847",293   "language": "Python",294   "lines": 223,295   "truncated": false,296   "block": 20,297   "row": 19542298  },299  {300   "path": "brie/utils/gtf_utils.py",301   "sha256": "e78959ff9bc345d05c066a6d84755f57e7d6c123b33e36890f074b30f56fce56",302   "language": "Python",303   "lines": 348,304   "truncated": false,305   "block": 20,306   "row": 20592307  },308  {309   "path": "brie/utils/io_utils.py",310   "sha256": "6a379351151e50ff7bef42323208cd23b5dc5cba0a312c6f9253bdd9d558fccc",311   "language": "Python",312   "lines": 199,313   "truncated": false,314   "block": 20,315   "row": 18842316  },317  {318   "path": "brie/utils/preprocessing.py",319   "sha256": "9181adaf58c938b78e661b8649341746cdbb5a91eccb6554a046cbc50a026b5c",320   "language": "Python",321   "lines": 83,322   "truncated": false,323   "block": 20,324   "row": 17339325  },326  {327   "path": "brie/utils/run_utils.py",328   "sha256": "3d5d81c3c3891ffa52efcc62448dc6f476d5f7b8cfb2675e4070d8a822020ada",329   "language": "Python",330   "lines": 206,331   "truncated": false,332   "block": 20,333   "row": 19337334  },335  {336   "path": "brie/utils/sam_utils.py",337   "sha256": "e02099de6cde241a1811165705fe09c0572092e892c786b99a5d89ab09addefa",338   "language": "Python",339   "lines": 229,340   "truncated": false,341   "block": 20,342   "row": 19535343  },344  {345   "path": "brie/utils/tran_utils.py",346   "sha256": "cf33c272aadcd41f8a89e5e5785a516d4eeeb4fe8d0f90687f3b335383e73605",347   "language": "Python",348   "lines": 331,349   "truncated": false,350   "block": 20,351   "row": 21020352  },353  {354   "path": "brie/version.py",355   "sha256": "60f79196f20b9e71ac7e7ebce679eaadc7c6a01dd7707d4e587f22a92db8a7ef",356   "language": "Python",357   "lines": 2,358   "truncated": false,359   "block": 20,360   "row": 12214361  },362  {363   "path": "brie/version1/brie.py",364   "sha256": "77435ce86ce278aa719e32fc7747744f5ad4fba6883a15da6ce2a782df0f1741",365   "language": "Python",366   "lines": 280,367   "truncated": false,368   "block": 20,369   "row": 20348370  },371  {372   "path": "brie/version1/brie_diff.py",373   "sha256": "221c4c7b4e93b0b04ea44c35ab7e81fa55ce9599bd35c9608426509a1d67f9fb",374   "language": "Python",375   "lines": 276,376   "truncated": false,377   "block": 20,378   "row": 19996379  },380  {381   "path": "brie/version1/model_brie.py",382   "sha256": "1fd02fdd0af4ab19befeb54fbdadc71adb96adc094b065bac7dd20fab0939e95",383   "language": "Python",384   "lines": 452,385   "truncated": false,386   "block": 20,387   "row": 21189388  },389  {390   "path": "doc/conf.py",391   "sha256": "abbe22d51001c226200d9e70e1be6c425418e777279462c1c3d6753f99fcb967",392   "language": "Python",393   "lines": 386,394   "truncated": false,395   "block": 20,396   "row": 20615397  },398  {399   "path": "examples/brie2_demo.sh",400   "sha256": "2ddb02a76b042a4253c28a6bd4a1dc8be52070e39532f174a0512bc8b919dc83",401   "language": "Shell",402   "lines": 40,403   "truncated": false,404   "block": 21,405   "row": 2219406  },407  {408   "path": "examples/demo_v1/anno_maker.sh",409   "sha256": "3810c828540a879e260280904d1aed269b8d62511358c6afcdead95bc1f54aa8",410   "language": "Shell",411   "lines": 67,412   "truncated": false,413   "block": 21,414   "row": 2627415  },416  {417   "path": "examples/demo_v1/brie_demo.sh",418   "sha256": "4f5ba00d54e5e1765f58cd7f9fa8c91b7b250075929967f8de00b4753919cf1a",419   "language": "Shell",420   "lines": 33,421   "truncated": false,422   "block": 21,423   "row": 2247424  },425  {426   "path": "examples/gastrulation/brie_sashimi.sh",427   "sha256": "18716ac371b95e33b1be765dc0076f3aee1a2bb3acc01e1bf18cce0b8039630f",428   "language": "Shell",429   "lines": 22,430   "truncated": false,431   "block": 21,432   "row": 2099433  },434  {435   "path": "examples/gastrulation/gastrulation_130cells.sh",436   "sha256": "9196a0801331a43c1e29ed29a371b50a0f53219d321a168fa313a0561d6da0df",437   "language": "Shell",438   "lines": 78,439   "truncated": false,440   "block": 21,441   "row": 2444442  },443  {444   "path": "examples/gastrulation/prepare_anno.sh",445   "sha256": "726deb117e72ee977ea0100e22fe72299cfc99541f2252110ac24b410ab1e331",446   "language": "Shell",447   "lines": 23,448   "truncated": false,449   "block": 21,450   "row": 2102451  },452  {453   "path": "examples/make_list.sh",454   "sha256": "5eb70c541d04aff789d6603d4c2a767716d2c3820d9e5f0f041d9426f7ca19a1",455   "language": "Shell",456   "lines": 14,457   "truncated": false,458   "block": 21,459   "row": 1869460  },461  {462   "path": "setup.py",463   "sha256": "128d91f0065de69e2139d5c78655406e00300858bbb993f5ac4f44855e2ddae7",464   "language": "Python",465   "lines": 77,466   "truncated": false,467   "block": 20,468   "row": 15890469  },470  {471   "path": "simulator/simuDropout.py",472   "sha256": "53f1bfd631fc85d48327a6de876c8e981009b0cbb14cfdbded805c429722e563",473   "language": "Python",474   "lines": 217,475   "truncated": false,476   "block": 20,477   "row": 19451478  },479  {480   "path": "simulator/simuPSI.py",481   "sha256": "c4d2d806db19c2dae994694c4e36692984c8efe5609ef8526af6c9122fa3028b",482   "language": "Python",483   "lines": 194,484   "truncated": false,485   "block": 20,486   "row": 19334487  },488  {489   "path": "simulator/spanki_demo.sh",490   "sha256": "a93eeb9d4f176d0dcc340ee4c108eafaea9a7675c62d502d8265f8c3ca59d48e",491   "language": "Shell",492   "lines": 50,493   "truncated": false,494   "block": 21,495   "row": 2439496  },497  {498   "path": "simulator/utils.py",499   "sha256": "9584f946bbc8ad48902a44eaa621f5283f952d62b7c839199eb7de5d8d9dd4a4",500   "language": "Python",501   "lines": 81,502   "truncated": false,503   "block": 20,504   "row": 15774505  }506 ]507}