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__zunpengliu__multi-region_ad.json264 linesDownload Raw Back to d7
1{2 "format": "oscr-script-manifest/1",3 "repository": "github.com/zunpengliu/multi-region_ad",4 "url": "https://github.com/ZunpengLiu/Multi-region_AD",5 "host": "github.com",6 "commit": "b4a49e97bcb34fbbaee10f6879f4ad86c925f2f8",7 "license": "MIT",8 "license_confirmed_by": "license file LICENSE",9 "redistribution": "yes",10 "files": [11  {12   "path": "01_snATAC/01_Integration_Processing/Python_Muon_Scanpy/Generate_TileMatrix.h5ad.py",13   "sha256": "76952350a7741cb67b3ec456ae13adec73201d08ac3a7ad74e65c6b1c6585ce6",14   "language": "Python",15   "lines": 80,16   "truncated": false,17   "block": 19,18   "row": 1041119  },20  {21   "path": "01_snATAC/01_Integration_Processing/Python_Muon_Scanpy/snATAC_Integration_processing.py",22   "sha256": "0049d26750f3bb11262a234e39aa9524521cf406c3220e893df7a4cda4190ad6",23   "language": "Python",24   "lines": 164,25   "truncated": false,26   "block": 19,27   "row": 1268128  },29  {30   "path": "01_snATAC/01_Integration_Processing/R_ArchR/01_ArchR_Generate_Arrows.R",31   "sha256": "60383bec4f6a0ac8277f48bc0d55d5564db881fffce11f9eeadfc59aadbbe356",32   "language": "R",33   "lines": 39,34   "truncated": false,35   "block": 19,36   "row": 1471537  },38  {39   "path": "01_snATAC/01_Integration_Processing/R_ArchR/02_ArchR_Generate_Proj_QC_1st_UMAP.R",40   "sha256": "e7a8bb15340070cffe87dafd615c2287a11fff9935ec29a558119d3c4e726b30",41   "language": "R",42   "lines": 108,43   "truncated": false,44   "block": 19,45   "row": 1480846  },47  {48   "path": "01_snATAC/01_Integration_Processing/R_ArchR/03_ArchR_High-Quality_Cell_Subsetting_and_Dimensionality_Reduction.R",49   "sha256": "d7dc870ce28a3359b551d45217a90a02ff761bd7e5b14a0807bcc797823f9cd1",50   "language": "R",51   "lines": 136,52   "truncated": false,53   "block": 19,54   "row": 1487955  },56  {57   "path": "01_snATAC/01_Integration_Processing/R_ArchR/04_ArchR_GeneScore_Marker_Genes.R",58   "sha256": "7c7f26cbe108042ada2e9e969883288c5a2f05884a86c10f6a06860a58ff3747",59   "language": "R",60   "lines": 95,61   "truncated": false,62   "block": 19,63   "row": 1480364  },65  {66   "path": "01_snATAC/01_Integration_Processing/R_ArchR/05_ArchR_BigWig_Generation.R",67   "sha256": "9405fb997ee2ab5b4c3c7ed0af2de3f44dd48a2e78d19ad5f4f2f1d4b066d197",68   "language": "R",69   "lines": 34,70   "truncated": false,71   "block": 19,72   "row": 1469673  },74  {75   "path": "01_snATAC/01_Integration_Processing/R_ArchR/06_ArchR_Peak_Calling.R",76   "sha256": "db2bb63a47309dfceb8e8bdcd83ebaf54410a0069812871c0e4b5c917760a00a",77   "language": "R",78   "lines": 83,79   "truncated": false,80   "block": 19,81   "row": 1477682  },83  {84   "path": "01_snATAC/01_Integration_Processing/R_ArchR/07_ArchR_Motif_Deviation.R",85   "sha256": "4691777875f2ef6760398cde6de2dd51cce3ac2a42e217ba8191d11c8f54c8ef",86   "language": "R",87   "lines": 84,88   "truncated": false,89   "block": 19,90   "row": 1479491  },92  {93   "path": "01_snATAC/02_cCRE_modules/NMF_cCRE_modules.py",94   "sha256": "276cf3e5c403059c5a66d49e5b90d6121b97d7f0d989a0899fb349cd3f82515d",95   "language": "Python",96   "lines": 116,97   "truncated": false,98   "block": 19,99   "row": 10971100  },101  {102   "path": "01_snATAC/03_Epigenomic_Compartments/01_HMMt_Epigenomic_Compartments.R",103   "sha256": "2c202fef113b15cd325d888ea90184758591cf3a3a299afbc9194d1331961005",104   "language": "R",105   "lines": 181,106   "truncated": false,107   "block": 19,108   "row": 14940109  },110  {111   "path": "01_snATAC/03_Epigenomic_Compartments/02_Compartment_100kb_Embedding.py",112   "sha256": "df3b66605ad84cd3eb5e4f9a0d39187c9f3c2079b6612b84674a9ee22d2aea09",113   "language": "Python",114   "lines": 166,115   "truncated": false,116   "block": 19,117   "row": 12365118  },119  {120   "path": "01_snATAC/03_Epigenomic_Compartments/Fold_Enrichment_of_Features_across_Genomic_Bins.py",121   "sha256": "4bf2709d4be37eb2793cee552b802e085445092983b8a276bc778548b9ad76c1",122   "language": "Python",123   "lines": 143,124   "truncated": false,125   "block": 19,126   "row": 12572127  },128  {129   "path": "01_snATAC/04_Epigenomic_Information/01_Separate_Chromatin_States.py",130   "sha256": "4f84e0884f8b9b770959e46dc79513326fb1732c632bf0e41e572c35b646725f",131   "language": "Python",132   "lines": 18,133   "truncated": false,134   "block": 19,135   "row": 8920136  },137  {138   "path": "01_snATAC/04_Epigenomic_Information/02_Reads_in_Chromatin_States.R",139   "sha256": "e377da71c11d85809566d6258e4fb8de31bb517c811e0f8491e17bb755c67b5d",140   "language": "R",141   "lines": 76,142   "truncated": false,143   "block": 19,144   "row": 14764145  },146  {147   "path": "01_snATAC/04_Epigenomic_Information/03_Chromatin_State_based_Epigenomic_Information_Score.py",148   "sha256": "30858f974137d4315e972c41cce00f18c9393526225c86f3d7c808483d6f48e7",149   "language": "Python",150   "lines": 57,151   "truncated": false,152   "block": 19,153   "row": 9945154  },155  {156   "path": "01_snATAC/05_Differentially_Accessible_Region(DAR)/snATAC.DAR.Nebula.R",157   "sha256": "168b6f669054e3f4bd14353d88033c01cc819b8475c7263fd3f7baf7f8a9c808",158   "language": "R",159   "lines": 87,160   "truncated": false,161   "block": 19,162   "row": 14861163  },164  {165   "path": "01_snATAC/06_Cell-type_Composition_Changes/CellType_Compositional_Changes_with_Pathology.R",166   "sha256": "7712d4447f678c327f68bad8b6d3b2755007b6f69bdefd1b08c910eb02f6309d",167   "language": "R",168   "lines": 302,169   "truncated": false,170   "block": 19,171   "row": 15044172  },173  {174   "path": "01_snATAC/07_Functional_Enrichment/ChromHMM_enrichment.sh",175   "sha256": "39e5091469fd080ccbe74a41073104dacb876115f60e2ae11bc49e53a0974141",176   "language": "Shell",177   "lines": 45,178   "truncated": false,179   "block": 19,180   "row": 15616181  },182  {183   "path": "01_snATAC/07_Functional_Enrichment/GREAT_Functional_enrichment.R",184   "sha256": "176a2f6a90cdf206cbb1b4b900ea55d5f2f69b281d95764039799194b12d4f7a",185   "language": "R",186   "lines": 43,187   "truncated": false,188   "block": 19,189   "row": 14725190  },191  {192   "path": "01_snATAC/08_GWAS_enrichment/Liftover_hg38_to_hg19.sh",193   "sha256": "f5099a31854e7b5a6d50badaf259b7ffcec3f49e4b59da8120078da034b554af",194   "language": "Shell",195   "lines": 10,196   "truncated": false,197   "block": 19,198   "row": 15291199  },200  {201   "path": "01_snATAC/08_GWAS_enrichment/run_LDSC.py",202   "sha256": "afdceb5b7291fea800b904d07b46872bb64e385410ed305aab5094a1a40a463a",203   "language": "Python",204   "lines": 162,205   "truncated": false,206   "block": 19,207   "row": 12559208  },209  {210   "path": "01_snATAC/08_GWAS_enrichment/run_SCANVAGE.R",211   "sha256": "8846e1d4f2d3fdfae6edbc0fbca2a6b29914095fc83e27a788ed92e3ec5d0274",212   "language": "R",213   "lines": 112,214   "truncated": false,215   "block": 19,216   "row": 14924217  },218  {219   "path": "02_snRNA/01_Integration_Processing/snRNA_integration.py",220   "sha256": "145caccf5f3667258052f59b05b0ef66af7ccb8e4e9a37e7cf573ad1b2660946",221   "language": "Python",222   "lines": 163,223   "truncated": false,224   "block": 19,225   "row": 12167226  },227  {228   "path": "02_snRNA/02_Differentially_Expressed_Genes(DEGs)/Nebula_DEGs.R",229   "sha256": "519b7f2fd8b7269e1538805d57712ec5ef69bbe11e67b39c1fa53e6c6cf7044b",230   "language": "R",231   "lines": 85,232   "truncated": false,233   "block": 19,234   "row": 14812235  },236  {237   "path": "02_snRNA/03_Functional_enrichment/EnrichR.R",238   "sha256": "46f13d70f16721d1604d6d9e53ff1ee1b3d4991339667c7fdb2509c621b60017",239   "language": "R",240   "lines": 94,241   "truncated": false,242   "block": 19,243   "row": 14792244  },245  {246   "path": "LICENSE",247   "sha256": "3c018752f316d99229f0a773234885eeb1144353721c92a8ea293db9c7436b4a",248   "language": "License",249   "lines": 21,250   "truncated": false,251   "block": 19,252   "row": 4189253  },254  {255   "path": "README.md",256   "sha256": "2b5485b094041ee89a6ec06a3d8244ab3acd41af5567178803db627dd01eea56",257   "language": "Text",258   "lines": 3,259   "truncated": false,260   "block": 19,261   "row": 16026262  }263 ]264}