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
rootmanifestseegithub.com__cxtaslim__rna-seqezpz.json
github.com__cxtaslim__rna-seqezpz.json372 linesDownload Raw Back to ee
1{2 "format": "oscr-script-manifest/1",3 "repository": "github.com/cxtaslim/rna-seqezpz",4 "url": "https://github.com/cxtaslim/RNA-SeqEZPZ",5 "host": "github.com",6 "commit": "47eda7e020f1cee270fd3a92446bf7655ada29d1",7 "license": "CC-BY-NC-ND-4.0",8 "license_confirmed_by": "license file LICENSE",9 "redistribution": "with_conditions",10 "files": [11  {12   "path": "LICENSE",13   "sha256": "f7f28b8c7a1af76b9874ca6d040e8b1eb6768fd1043106c9d315090ea96754e7",14   "language": "License",15   "lines": 402,16   "truncated": false,17   "block": 6,18   "row": 210319  },20  {21   "path": "README.md",22   "sha256": "5afd970411dac8db4b25cf18fb321769e042fdf5a045cbdb196421bb76aca878",23   "language": "Text",24   "lines": 304,25   "truncated": false,26   "block": 21,27   "row": 327428  },29  {30   "path": "project_ex_out/outputs/logs/scripts/run_align_create_tracks_rna.sh",31   "sha256": "7e5bb2a8eedfa273a71a355a8cb8e5f492568cd22e82e71f52047ebf131c3125",32   "language": "Shell",33   "lines": 571,34   "truncated": false,35   "block": 21,36   "row": 278237  },38  {39   "path": "project_ex_out/outputs/logs/scripts/run_differential_analysis_rna.sh",40   "sha256": "be6e9b604b517572d018cd3137e7cb1454904a3c6f1f50275f642228f83815bd",41   "language": "Shell",42   "lines": 333,43   "truncated": false,44   "block": 21,45   "row": 276146  },47  {48   "path": "project_ex_out/outputs/logs/scripts/run_rnaseq_full.sh",49   "sha256": "f47046f651bdd7f12802dc0a6d9c4a657110bccabcad5fc9ccdf177fbf66b408",50   "language": "Shell",51   "lines": 430,52   "truncated": false,53   "block": 21,54   "row": 277855  },56  {57   "path": "project_ex_out/outputs/logs/scripts/run_star_index.sh",58   "sha256": "3470659d950dd007e24dcfd09b0940c051960d08f5b7bf56378702fdf31ae397",59   "language": "Shell",60   "lines": 315,61   "truncated": false,62   "block": 21,63   "row": 275964  },65  {66   "path": "project_ex_out/outputs/logs/scripts/run_trim_qc.sh",67   "sha256": "fcdc457bedfe469ad7557b6ef1b3ae6cbf53f7aaaff477cfba785fa2af330daf",68   "language": "Shell",69   "lines": 315,70   "truncated": false,71   "block": 21,72   "row": 275873  },74  {75   "path": "scripts/app.R",76   "sha256": "bfdffe5dbd8be406f91e7d5c0117971817ddf354a384400e82cd3b76b65f3a40",77   "language": "R",78   "lines": 3863,79   "truncated": false,80   "block": 21,81   "row": 161282  },83  {84   "path": "scripts/app_1.R",85   "sha256": "ddf0cb8b7310ba6226f03e7e90e9d24fadc52c4fed5b65f57acfe6d0dc983b38",86   "language": "R",87   "lines": 94,88   "truncated": false,89   "block": 21,90   "row": 88691  },92  {93   "path": "scripts/app_2.R",94   "sha256": "866fd0a1b2cfc52b1351f3223d0156ce2f970af7f71e0cc2c695215e9506ac55",95   "language": "R",96   "lines": 31,97   "truncated": false,98   "block": 21,99   "row": 624100  },101  {102   "path": "scripts/app_3.R",103   "sha256": "85c97ddc6039376d2c513971491510b8f6714e96e97d67ed3df311314170c7f4",104   "language": "R",105   "lines": 35,106   "truncated": false,107   "block": 21,108   "row": 605109  },110  {111   "path": "scripts/app_simg.sh",112   "sha256": "04eee7a81f975d594df542dee8c81da107b3373ec47196d567c04a59fd044b79",113   "language": "Shell",114   "lines": 6,115   "truncated": false,116   "block": 21,117   "row": 1838118  },119  {120   "path": "scripts/check_job.sh",121   "sha256": "9381b1143c6587845dc58c5581ef1f2b65a9483d2040cd8acbfca611458b0ea3",122   "language": "Shell",123   "lines": 82,124   "truncated": false,125   "block": 21,126   "row": 2625127  },128  {129   "path": "scripts/internal_R/MAPlot.R",130   "sha256": "1c33fabb363259eeacbc05d9229f3e05a609fc53ab4428a254854983bda14cf0",131   "language": "R",132   "lines": 30,133   "truncated": false,134   "block": 21,135   "row": 752136  },137  {138   "path": "scripts/internal_R/PCAPlot.R",139   "sha256": "09664b07dc2d0f65481063748787aba3ce67c33569808d182c719c4b49e155b8",140   "language": "R",141   "lines": 87,142   "truncated": false,143   "block": 21,144   "row": 954145  },146  {147   "path": "scripts/internal_R/calcDiffTotal.R",148   "sha256": "8a0637fc9d7033fcebad4ec5605496c6c3be649eb0511b9f5e3d27ced4d9f491",149   "language": "R",150   "lines": 31,151   "truncated": false,152   "block": 21,153   "row": 695154  },155  {156   "path": "scripts/internal_R/descriptionPlots.R",157   "sha256": "31e35f715c14f99ba7975c13d99e11855a3bf4c6039b3121d61988bdad809d1f",158   "language": "R",159   "lines": 16,160   "truncated": false,161   "block": 21,162   "row": 619163  },164  {165   "path": "scripts/internal_R/diffPlot.R",166   "sha256": "c8f02dd15dfc44bfeb1851f1448c39b04d746648c590bcf44c4a0989749c43cc",167   "language": "R",168   "lines": 101,169   "truncated": false,170   "block": 21,171   "row": 1015172  },173  {174   "path": "scripts/internal_R/exploreCounts.R",175   "sha256": "960180aaeb660cd4e96c626182c33e4e99390ba45ef1e06d64038b4aaa47b53e",176   "language": "R",177   "lines": 24,178   "truncated": false,179   "block": 21,180   "row": 630181  },182  {183   "path": "scripts/internal_R/exportResults.DESeq2.R",184   "sha256": "1b5be73c66fb2b9b135f117a7ba49db8e364ce5de2980a4f9042ec88f294c159",185   "language": "R",186   "lines": 104,187   "truncated": false,188   "block": 21,189   "row": 1078190  },191  {192   "path": "scripts/internal_R/getDiffTop.R",193   "sha256": "35ea31deda2b6cf1a459015a7b986256b34f79e8d9e9fa7a90d7fc4933f51bcb",194   "language": "R",195   "lines": 49,196   "truncated": false,197   "block": 21,198   "row": 947199  },200  {201   "path": "scripts/internal_R/loadTargetFile.R",202   "sha256": "281b182657527c474a2d9aa1ca424b8ed3dfc49964cd422fa00cdf7f0f2de5d2",203   "language": "R",204   "lines": 34,205   "truncated": false,206   "block": 21,207   "row": 816208  },209  {210   "path": "scripts/internal_R/pairwiseScatterPlots.R",211   "sha256": "f439fb09fb7ff8fdc8097dc26cc795d3fd43ba6d2c0f77bd6823b47688819a5f",212   "language": "R",213   "lines": 40,214   "truncated": false,215   "block": 21,216   "row": 749217  },218  {219   "path": "scripts/internal_R/rawpHist.R",220   "sha256": "fbb60aca3080419f19e53130cdc135afbce8bc762940c6e3ee10b50efeb132ed",221   "language": "R",222   "lines": 44,223   "truncated": false,224   "block": 21,225   "row": 849226  },227  {228   "path": "scripts/internal_R/report_DESeq2.rmd",229   "sha256": "28b50bdfb2a03c6a4a041788005fb7a597ef96809cffffa954c99457e5c5317f",230   "language": "R",231   "lines": 334,232   "truncated": false,233   "block": 21,234   "row": 1492235  },236  {237   "path": "scripts/internal_R/run.DESeq2.R",238   "sha256": "b16a45e26942583184d7c3fb3880d826c08fcb26cdee1e37e48c998e2e359b5a",239   "language": "R",240   "lines": 28,241   "truncated": false,242   "block": 21,243   "row": 727244  },245  {246   "path": "scripts/internal_R/summarizeResults.DESeq2.R",247   "sha256": "ee48d1771556f3a7f56758d80038ad0a67fa64f6d684723ef6d2c11eefc070c5",248   "language": "R",249   "lines": 46,250   "truncated": false,251   "block": 21,252   "row": 815253  },254  {255   "path": "scripts/internal_R/volcanoPlot.R",256   "sha256": "c60dd96b35fa83b35d1e74808f9f97c2b47ab4ca2e1b0a5da1ff10ffe7c88ba8",257   "language": "R",258   "lines": 25,259   "truncated": false,260   "block": 21,261   "row": 705262  },263  {264   "path": "scripts/internal_R/writeReport.DESeq2.R",265   "sha256": "3567064a2c92e9b46307e352ec5216dee012d574befbc60a3df4bc24f7856741",266   "language": "R",267   "lines": 13,268   "truncated": false,269   "block": 21,270   "row": 597271  },272  {273   "path": "scripts/run_align_create_tracks_rna.sh",274   "sha256": "014a4060ca1c7635c4a3bb6d7db8f7b21fa42ea6b68bd20b4227c08b4c19ff5f",275   "language": "Shell",276   "lines": 597,277   "truncated": false,278   "block": 21,279   "row": 2785280  },281  {282   "path": "scripts/run_chrome.sh",283   "sha256": "a1de8b96d5d79a957a4a6870a83105b25130f1613b4a21edcbe7073b0e290862",284   "language": "Shell",285   "lines": 6,286   "truncated": false,287   "block": 21,288   "row": 1872289  },290  {291   "path": "scripts/run_differential_analysis_rna.sh",292   "sha256": "65b9a6349d3171ee3c1ec84d31e5294a0adf2784262d79d15122f511cfebed66",293   "language": "Shell",294   "lines": 345,295   "truncated": false,296   "block": 21,297   "row": 2764298  },299  {300   "path": "scripts/run_firefox.sh",301   "sha256": "b5823dc7e9ab6d0afb3487c45e3780ce48706c84cf60ff710b3f6480a54a3cff",302   "language": "Shell",303   "lines": 12,304   "truncated": false,305   "block": 21,306   "row": 1955307  },308  {309   "path": "scripts/run_listen_app.sh",310   "sha256": "57e9179fc5d97ef4d2e1fcf3cd3f76657f74ca1971d964571a77928f6b5ec610",311   "language": "Shell",312   "lines": 21,313   "truncated": false,314   "block": 21,315   "row": 2014316  },317  {318   "path": "scripts/run_rnaseq_full.sh",319   "sha256": "4030d460c93b0bd724f0c5266f6cabea46c043838e8e6f0e38dfe74b81acf9c8",320   "language": "Shell",321   "lines": 444,322   "truncated": false,323   "block": 21,324   "row": 2779325  },326  {327   "path": "scripts/run_shiny_analysis.sh",328   "sha256": "7c0714c6690578b21b8831bb220734a5460303c8f1992f3d410715575b5adc3c",329   "language": "Shell",330   "lines": 234,331   "truncated": false,332   "block": 21,333   "row": 2736334  },335  {336   "path": "scripts/run_star_index.sh",337   "sha256": "21f0aa472d6164be2f643c071272e550b327768c10aec08f9346f8314ddc4847",338   "language": "Shell",339   "lines": 322,340   "truncated": false,341   "block": 21,342   "row": 2762343  },344  {345   "path": "scripts/run_trim_qc.sh",346   "sha256": "b286626bcf51d0e99680a54966dcd08d881f97f7200e5923148baadb3b56a6c5",347   "language": "Shell",348   "lines": 296,349   "truncated": false,350   "block": 21,351   "row": 2750352  },353  {354   "path": "scripts/slurm_config_var.sh",355   "sha256": "8030ae9df46fbf728251f74da8a08286132aedb6989483d01e6334e80823e74d",356   "language": "Shell",357   "lines": 14,358   "truncated": false,359   "block": 21,360   "row": 1999361  },362  {363   "path": "scripts/template_script_DESeq2_simg.R",364   "sha256": "8a4e91c6ed4267bce377a5aaad11cdb2fecbe39eeb8fc323d624f0ee9de32c5e",365   "language": "R",366   "lines": 234,367   "truncated": false,368   "block": 21,369   "row": 1270370  }371 ]372}