OpenScientificCodeRegistry/Database

1{2 "format": "oscr-script-manifest/1",3 "repository": "github.com/dmcable/spacexr",4 "url": "https://github.com/dmcable/spacexr/blob/master/vignettes/spatial-transcriptomics.Rmd",5 "host": "github.com",6 "commit": "9f5dc33c8060f946c6072a138b70e189636e1435",7 "license": "GPL-3.0",8 "license_confirmed_by": "license file LICENSE",9 "redistribution": "yes",10 "files": [11  {12   "path": "AnalysisCSIDE/Figures/figure2.Rmd",13   "sha256": "ca13481def4f66bb823e2f5e2c4098c32549586ddf282f2afdd27bcaf7324fc7",14   "language": "R",15   "lines": 349,16   "truncated": false,17   "block": 1,18   "row": 1052619  },20  {21   "path": "AnalysisCSIDE/Figures/figure3.Rmd",22   "sha256": "b16f6511233f47d6a51c4e4aae714a15b8559e6f5d5a2f2e4c007bb27d56e0ad",23   "language": "R",24   "lines": 180,25   "truncated": false,26   "block": 1,27   "row": 1041428  },29  {30   "path": "AnalysisCSIDE/Figures/figure4_j20.Rmd",31   "sha256": "9e233d09fd48f17d269290f78a90a38905266e20345dd64b40c80bfb1ac2edf8",32   "language": "R",33   "lines": 203,34   "truncated": false,35   "block": 1,36   "row": 1043037  },38  {39   "path": "AnalysisCSIDE/Figures/figure4_merfish.Rmd",40   "sha256": "15558e8e659cf24d78755fc9e7f98f652d9b62ef7cf75297d3e25f510b5e48ed",41   "language": "R",42   "lines": 287,43   "truncated": false,44   "block": 1,45   "row": 1052946  },47  {48   "path": "AnalysisCSIDE/Figures/figure4_testes.Rmd",49   "sha256": "043d3ab00ab353088c9e26ad787bc5adb765de2f09e53f35b8b3eeee8e253826",50   "language": "R",51   "lines": 315,52   "truncated": false,53   "block": 1,54   "row": 1050055  },56  {57   "path": "AnalysisCSIDE/Figures/figure4_visium.Rmd",58   "sha256": "5badb7637ec2f78634951707881a93ee4d1f04cbbb164d9a1d85b1494bc54a76",59   "language": "R",60   "lines": 206,61   "truncated": false,62   "block": 1,63   "row": 1046264  },65  {66   "path": "AnalysisCSIDE/Figures/figure5_nonparametric.Rmd",67   "sha256": "2048bcf7bb95a2553e039cfdc6821608914fc27036f741dc47073ab3789ed8dc",68   "language": "R",69   "lines": 254,70   "truncated": false,71   "block": 1,72   "row": 1044273  },74  {75   "path": "AnalysisCSIDE/Figures/figure5_parametric.Rmd",76   "sha256": "bbef2712ddd9664cc100d2dd2a56a93c211d7543b3ff4e52b3c681b00ac070e3",77   "language": "R",78   "lines": 213,79   "truncated": false,80   "block": 1,81   "row": 1046782  },83  {84   "path": "AnalysisCSIDE/Figures/supp1.Rmd",85   "sha256": "4515e6b1ed950e8024f4039168084d319279e7ba86147da46001dd0fbff01b0d",86   "language": "R",87   "lines": 478,88   "truncated": false,89   "block": 1,90   "row": 1057191  },92  {93   "path": "AnalysisCSIDE/Figures/supp2.Rmd",94   "sha256": "5d5cd24dee38b3b20963ca326ab6012a0c3bd4d0b15bb5f22c69330ce7123179",95   "language": "R",96   "lines": 215,97   "truncated": false,98   "block": 1,99   "row": 10435100  },101  {102   "path": "AnalysisCSIDE/Figures/supp3.Rmd",103   "sha256": "02acf39d0f097c3bef2a9aa6f9d532912379f06d59524176ba1d8921afb228f0",104   "language": "R",105   "lines": 180,106   "truncated": false,107   "block": 1,108   "row": 10352109  },110  {111   "path": "AnalysisCSIDE/Figures/supp4.Rmd",112   "sha256": "8aab489f0f4109dce666b67f1692eed0d4d373f1b59b932ce1096cf81c9dd016",113   "language": "R",114   "lines": 92,115   "truncated": false,116   "block": 1,117   "row": 10260118  },119  {120   "path": "AnalysisCSIDE/Figures/supp5.Rmd",121   "sha256": "1839222fd9d8c7f5fe830358e0b0a62623751ba3c6dbf22d9d147529706150fb",122   "language": "R",123   "lines": 364,124   "truncated": false,125   "block": 1,126   "row": 10523127  },128  {129   "path": "AnalysisCSIDE/Figures/supp6.Rmd",130   "sha256": "67dc76d6b07c2858db3dca1145dfacf5966e693dd813a360cc1ab6f2038978ea",131   "language": "R",132   "lines": 81,133   "truncated": false,134   "block": 1,135   "row": 10173136  },137  {138   "path": "AnalysisCSIDE/Figures/supp7.Rmd",139   "sha256": "cb95728c988431012d774ebbf58d18c2fb16a8f3c4ba9bc419d0211e6e6a4cbf",140   "language": "R",141   "lines": 212,142   "truncated": false,143   "block": 1,144   "row": 10421145  },146  {147   "path": "AnalysisCSIDE/Figures/supp8.Rmd",148   "sha256": "3f53fe6ee9e7ff1225db9e0af65591cd242312427bb5b609cf54ee712ddeb437",149   "language": "R",150   "lines": 166,151   "truncated": false,152   "block": 1,153   "row": 10351154  },155  {156   "path": "AnalysisCSIDE/Preprocessing_and_RCTD/cer_reps.R",157   "sha256": "8b43516a5ac225943426613c3e009d6804b88cc0af93e3fc8b0185605d9709c7",158   "language": "R",159   "lines": 90,160   "truncated": false,161   "block": 1,162   "row": 10221163  },164  {165   "path": "AnalysisCSIDE/Preprocessing_and_RCTD/run_RCTD_testes.R",166   "sha256": "25ef2e57b780ae112aa805547b18446a88fdc0cc62b8cae83d2dcbe34a5f3be8",167   "language": "R",168   "lines": 33,169   "truncated": false,170   "block": 1,171   "row": 10032172  },173  {174   "path": "AnalysisCSIDE/README.Rmd",175   "sha256": "c473770aac083c9adec41c59d229463d751e8bccdbaec8239c6f0d1783c5da85",176   "language": "R",177   "lines": 110,178   "truncated": false,179   "block": 1,180   "row": 10387181  },182  {183   "path": "AnalysisCSIDE/helper_functions/alzheimers_helper.R",184   "sha256": "4dbe6c0e7d2a771414e33c365d823bb854e09cca639cc1c85fae3218686b9ba1",185   "language": "R",186   "lines": 216,187   "truncated": false,188   "block": 1,189   "row": 10370190  },191  {192   "path": "AnalysisCSIDE/helper_functions/de_simulation_helper.R",193   "sha256": "7492049ba0d54ce5144cfb04de93e37d8665c232a8aeca4e8ce1ca1f5835c6ea",194   "language": "R",195   "lines": 135,196   "truncated": false,197   "block": 1,198   "row": 10348199  },200  {201   "path": "AnalysisCSIDE/helper_functions/merge_de_helper.R",202   "sha256": "1a2a756890cb98d7373494b7f4341d17830a3e5a9bfc6219069c1dff8bf59b23",203   "language": "R",204   "lines": 48,205   "truncated": false,206   "block": 1,207   "row": 10107208  },209  {210   "path": "AnalysisCSIDE/helper_functions/personal_utils.R",211   "sha256": "167e1d72416fb9e737a82b864943a9aa1c2f2b46eafd2d40f648e1f7751e6064",212   "language": "R",213   "lines": 35,214   "truncated": false,215   "block": 1,216   "row": 10065217  },218  {219   "path": "AnalysisCSIDE/helper_functions/testes_helper.R",220   "sha256": "6fecafa2d419452e6cbd64cadc266b17ff27001b03d88eaf79bebb9970845c05",221   "language": "R",222   "lines": 263,223   "truncated": false,224   "block": 1,225   "row": 10486226  },227  {228   "path": "AnalysisCSIDE/image_analysis/hcr.R",229   "sha256": "256d7ffde3047fa08a6f4b3199ec066b15bf741f15df499e5ce1211e93ff62c0",230   "language": "R",231   "lines": 110,232   "truncated": false,233   "block": 1,234   "row": 10133235  },236  {237   "path": "AnalysisCSIDE/image_analysis/overlay.R",238   "sha256": "b03c3985b7b235243d3db763bced4d909d867f9397770dfc34659eaa16703bf4",239   "language": "R",240   "lines": 27,241   "truncated": false,242   "block": 1,243   "row": 10014244  },245  {246   "path": "AnalysisCSIDE/j20/align_plaque_density.R",247   "sha256": "ca85a7d67f72ed8ac57dc569df9706cf5f48698e24c27cc77dc202523e8e0ab0",248   "language": "R",249   "lines": 58,250   "truncated": false,251   "block": 1,252   "row": 10123253  },254  {255   "path": "AnalysisCSIDE/j20/create_pd.R",256   "sha256": "9bfdb7cbe23e7a070d62cda52d44e7b4f8b8b3937af512a2d94a5a48774d2a8b",257   "language": "R",258   "lines": 14,259   "truncated": false,260   "block": 1,261   "row": 9944262  },263  {264   "path": "AnalysisCSIDE/j20/pd_to_exvar.R",265   "sha256": "fab4dd1ae3cfb9fb3f5703e6ded4e7af3f80f2c6ebcf8b8b0c5f9603a9f81ea8",266   "language": "R",267   "lines": 81,268   "truncated": false,269   "block": 1,270   "row": 10184271  },272  {273   "path": "AnalysisCSIDE/j20/preprocess_j20.R",274   "sha256": "dfc26175164905eee2a48760ce54d78b9f0830ba970eefedf1e3099ea454650f",275   "language": "R",276   "lines": 45,277   "truncated": false,278   "block": 1,279   "row": 10109280  },281  {282   "path": "AnalysisCSIDE/j20/run_CSIDE_j20_21.R",283   "sha256": "b023e43feaa5a635928e563cd1c545b9769f93531ad7fb52c458d236ae4dd10c",284   "language": "R",285   "lines": 14,286   "truncated": false,287   "block": 1,288   "row": 9951289  },290  {291   "path": "AnalysisCSIDE/j20/run_CSIDE_j20_22.R",292   "sha256": "01c1d244b8cefb869e9271136d4fd5d8ea9173f2b432b5c9c1274cf11128d979",293   "language": "R",294   "lines": 14,295   "truncated": false,296   "block": 1,297   "row": 9948298  },299  {300   "path": "AnalysisCSIDE/j20/run_CSIDE_j20_23.R",301   "sha256": "149922ada102d029422ba6f906e512daf9a891810cb43eb16d40928ec81541a8",302   "language": "R",303   "lines": 14,304   "truncated": false,305   "block": 1,306   "row": 9949307  },308  {309   "path": "AnalysisCSIDE/j20/run_CSIDE_j20_24.R",310   "sha256": "9888db7f41b9737903f71317b1880b0676b868f1b2a7aed2852433fded8d2b77",311   "language": "R",312   "lines": 14,313   "truncated": false,314   "block": 1,315   "row": 9950316  },317  {318   "path": "AnalysisCSIDE/j20/run_RCTD_j20_21.R",319   "sha256": "a3427765d658eedd16ef445e09f17a700b24002be89fd4447e6c8c5e50b41a5a",320   "language": "R",321   "lines": 20,322   "truncated": false,323   "block": 1,324   "row": 9969325  },326  {327   "path": "AnalysisCSIDE/j20/run_RCTD_j20_22.R",328   "sha256": "54c9395ccc994cbf18778124b59f50af333b29887870de4234a57feabdede2f8",329   "language": "R",330   "lines": 20,331   "truncated": false,332   "block": 1,333   "row": 9967334  },335  {336   "path": "AnalysisCSIDE/j20/run_RCTD_j20_23.R",337   "sha256": "822fd45b944a138d80ef899c0fdc618a7a36d4893c3bfbde106b17f4c8bca9e3",338   "language": "R",339   "lines": 20,340   "truncated": false,341   "block": 1,342   "row": 9968343  },344  {345   "path": "AnalysisCSIDE/j20/run_RCTD_j20_24.R",346   "sha256": "d768101e77b7c702653d6b4717ed426bb4022b34fcf2d0e6a828b71c2b538069",347   "language": "R",348   "lines": 20,349   "truncated": false,350   "block": 1,351   "row": 9970352  },353  {354   "path": "AnalysisCSIDE/run_CSIDE/run_de_cer_08.R",355   "sha256": "6f226348749bc7675957655f1f54b8ed4c0075691894607eea3d47730c8dc4b8",356   "language": "R",357   "lines": 49,358   "truncated": false,359   "block": 1,360   "row": 10140361  },362  {363   "path": "AnalysisCSIDE/run_CSIDE/run_de_cer_09.R",364   "sha256": "286faf4653bdab6a9a3adf9a66ae3b1d334e5e6a0381edc3f883ef54735a4378",365   "language": "R",366   "lines": 34,367   "truncated": false,368   "block": 1,369   "row": 10087370  },371  {372   "path": "AnalysisCSIDE/run_CSIDE/run_de_cer_11.R",373   "sha256": "cfb777bb94c77554181405aa31a31d79e273a4e69ee9d5421c7d308eb7d4d55f",374   "language": "R",375   "lines": 34,376   "truncated": false,377   "block": 1,378   "row": 10088379  },380  {381   "path": "AnalysisCSIDE/run_CSIDE/run_de_merfish.R",382   "sha256": "673da9c57e13ca8b54d2e8b7e6d73b47107ac14e55fa2a1fd3f34e9a5e60fadd",383   "language": "R",384   "lines": 190,385   "truncated": false,386   "block": 1,387   "row": 10373388  },389  {390   "path": "AnalysisCSIDE/run_CSIDE/run_de_nonparametric.R",391   "sha256": "ae7503c3dbd38de5a0fc3707c1323686744fd33efb56f4b6d94455acf3fb0379",392   "language": "R",393   "lines": 25,394   "truncated": false,395   "block": 1,396   "row": 9989397  },398  {399   "path": "AnalysisCSIDE/run_CSIDE/run_de_testes.R",400   "sha256": "dce7dad126564e63c7c04a0a6e952309b2fa246a954b5718e9acd7e136285fa8",401   "language": "R",402   "lines": 70,403   "truncated": false,404   "block": 1,405   "row": 10152406  },407  {408   "path": "AnalysisCSIDE/run_CSIDE/run_de_tumor.R",409   "sha256": "e5b963398dc67324762c54b3f84caab565103863f40a9b89da9a3bb4e3f67fe7",410   "language": "R",411   "lines": 138,412   "truncated": false,413   "block": 1,414   "row": 10343415  },416  {417   "path": "AnalysisPaper/MainFigures/Updated-Compatability/figure2-platform-effect.Rmd",418   "sha256": "0e25f28564b41fc0ea0a505d0ba96cb6fde8a3316570101285f062cc88a4e67e",419   "language": "R",420   "lines": 69,421   "truncated": false,422   "block": 1,423   "row": 10151424  },425  {426   "path": "AnalysisPaper/MainFigures/figure1.Rmd",427   "sha256": "900cc0d91780ed831b7d5d0bd79de413e3dea9c9fe8de9c143ebccb2f7e9d5bf",428   "language": "R",429   "lines": 155,430   "truncated": false,431   "block": 1,432   "row": 10374433  },434  {435   "path": "AnalysisPaper/MainFigures/figure2-platform-effect.Rmd",436   "sha256": "36966ccbf9987b23a9e3d445c3af50ea1e06638e35da63413946890b93c9bde5",437   "language": "R",438   "lines": 72,439   "truncated": false,440   "block": 1,441   "row": 10164442  },443  {444   "path": "AnalysisPaper/MainFigures/figure2.Rmd",445   "sha256": "8b1d173afaaaa4e47c629ec0c82b432abb9758f60239527402aa8e2746f240be",446   "language": "R",447   "lines": 192,448   "truncated": false,449   "block": 1,450   "row": 10418451  },452  {453   "path": "AnalysisPaper/MainFigures/figure3.Rmd",454   "sha256": "0e33762a3d2348fcf9ccd94410661a7e11562c0de42b3112cc141278a39c04ad",455   "language": "R",456   "lines": 285,457   "truncated": false,458   "block": 1,459   "row": 10509460  },461  {462   "path": "AnalysisPaper/MainFigures/figure4.Rmd",463   "sha256": "836f307991f36c5603c0bddb4652791af3b31ed34c6d34d14ee2b7b1dfcdda96",464   "language": "R",465   "lines": 214,466   "truncated": false,467   "block": 1,468   "row": 10491469  },470  {471   "path": "AnalysisPaper/MainFigures/figure5-all.Rmd",472   "sha256": "0f31af9ea6fc19daacfd0a3c5a8af4512e99041f42bc3994df3491ec34cf7811",473   "language": "R",474   "lines": 213,475   "truncated": false,476   "block": 1,477   "row": 10473478  },479  {480   "path": "AnalysisPaper/MainFigures/figure5-interneurons.Rmd",481   "sha256": "c7de66d7e26aced6510cf97caab1b88515d3f4141c72c1393bb626f07b52b2fa",482   "language": "R",483   "lines": 277,484   "truncated": false,485   "block": 1,486   "row": 10506487  },488  {489   "path": "AnalysisPaper/MainFigures/figure6-astrocytes.Rmd",490   "sha256": "50598043d66a07e7f0df724f471863ba07505ee8e3c8afd1522b742c70c1bbf6",491   "language": "R",492   "lines": 221,493   "truncated": false,494   "block": 1,495   "row": 10464496  },497  {498   "path": "AnalysisPaper/MainFigures/figure6-spatialgenes.Rmd",499   "sha256": "5affff25186417eab48821627365865f356e5318b63b54cfcfb08661961d42c4",500   "language": "R",501   "lines": 224,502   "truncated": false,503   "block": 1,504   "row": 10434505  },506  {507   "path": "AnalysisPaper/Plotting/figure_utils.R",508   "sha256": "b42a70f0166e30ca35a2e1db885c1d529efd0e052c38373c62ea105ccdaf611c",509   "language": "R",510   "lines": 262,511   "truncated": false,512   "block": 1,513   "row": 10494514  },515  {516   "path": "AnalysisPaper/README.Rmd",517   "sha256": "4d8ec315effade89954cf8af39baba1cd84164084870a1fd39f9a2e2985fe855",518   "language": "R",519   "lines": 70,520   "truncated": false,521   "block": 1,522   "row": 10286523  },524  {525   "path": "AnalysisPaper/Rscripts/doubletsimulation.R",526   "sha256": "98a1e522741b947193bc971b35ade57465f86b77c2efc7506798042e0ee95799",527   "language": "R",528   "lines": 61,529   "truncated": false,530   "block": 1,531   "row": 10178532  },533  {534   "path": "AnalysisPaper/Rscripts/dropSeqProcess.R",535   "sha256": "ff4a1feb8c1e8b586cd0e64db8b6b1811a2a7a96c70b741816872bd29b797275",536   "language": "R",537   "lines": 19,538   "truncated": false,539   "block": 1,540   "row": 9990541  },542  {543   "path": "AnalysisPaper/Rscripts/prepareNMF.R",544   "sha256": "112dc791afd9af0c4e5c2883543a4d573aa51734a3361cd4cc1ef0018b22a704",545   "language": "R",546   "lines": 30,547   "truncated": false,548   "block": 1,549   "row": 10026550  },551  {552   "path": "AnalysisPaper/Rscripts/processNMF.R",553   "sha256": "e3460cd880395a373a995d06406d102261c4123470b2d331b3eec55b3f7e9ce0",554   "language": "R",555   "lines": 20,556   "truncated": false,557   "block": 1,558   "row": 10000559  },560  {561   "path": "AnalysisPaper/Rscripts/processVisium.R",562   "sha256": "e5d377daa9fcb06428b5e2ebd61333a07d5530cac3030e3b8f6424873dec95f1",563   "language": "R",564   "lines": 33,565   "truncated": false,566   "block": 1,567   "row": 10086568  },569  {570   "path": "AnalysisPaper/Rscripts/subcluster.R",571   "sha256": "897a290c520f85fea87d6c7f5f4f7c84cb38d7d1b67522ccde8d7d833b4e8d6d",572   "language": "R",573   "lines": 91,574   "truncated": false,575   "block": 1,576   "row": 10289577  },578  {579   "path": "AnalysisPaper/Rscripts/weightDecompose.R",580   "sha256": "a10c418c664e0f2ab88158f1d2c0d308a93fa627fe298ea33a5ed5b8c77c903d",581   "language": "R",582   "lines": 30,583   "truncated": false,584   "block": 1,585   "row": 10036586  },587  {588   "path": "AnalysisPaper/SuppFigures/supp.Rmd",589   "sha256": "48e3282727aa06a4623dc2a5e9c904925d6381974601ec9cbe2909fd5021e263",590   "language": "R",591   "lines": 504,592   "truncated": false,593   "block": 1,594   "row": 10588595  },596  {597   "path": "AnalysisPaper/SuppFigures/supp_part2.Rmd",598   "sha256": "b08b1d7296929e81760e6279b328d2267d91e6f9988174dbc9c256affe7f76d0",599   "language": "R",600   "lines": 706,601   "truncated": false,602   "block": 1,603   "row": 10601604  },605  {606   "path": "LICENSE",607   "sha256": "3972dc9744f6499f0f9b2dbf76696f2ae7ad8af9b23dde66d6af86c9dfb36986",608   "language": "License",609   "lines": 674,610   "truncated": false,611   "block": 1,612   "row": 2235613  },614  {615   "path": "R/CSIDE.R",616   "sha256": "b434d876b5bad8fa07d2d6473f7b949d265ce856d0c534f7396ad295c0e02bb5",617   "language": "R",618   "lines": 748,619   "truncated": false,620   "block": 1,621   "row": 10606622  },623  {624   "path": "R/CSIDE_class.R",625   "sha256": "bdf3ea7c2342668415bebae210a6a82c208751da1a07a94e8b68fb78cba0da2f",626   "language": "R",627   "lines": 153,628   "truncated": false,629   "block": 1,630   "row": 10375631  },632  {633   "path": "R/CSIDE_helper.R",634   "sha256": "82e1e4b930dbbfe26b8cce99ecb49b861da7b45a2c6dfe46fe927a35805491b4",635   "language": "R",636   "lines": 223,637   "truncated": false,638   "block": 1,639   "row": 10390640  },641  {642   "path": "R/CSIDE_plots.R",643   "sha256": "c7164583dc0cb4c6c32a69b49ea62608aa4448f82f6a84c87f17c7002bf2cbe0",644   "language": "R",645   "lines": 524,646   "truncated": false,647   "block": 1,648   "row": 10575649  },650  {651   "path": "R/CSIDE_population.R",652   "sha256": "4a3c7b872d095b8d6ae67591a3f22a9ceaee6f4fe4f174213dee03bdba2e36a5",653   "language": "R",654   "lines": 206,655   "truncated": false,656   "block": 1,657   "row": 10403658  },659  {660   "path": "R/CSIDE_stats.R",661   "sha256": "e27804ddbbaee86354c032905d79d4f3ce95ff81ed21f939d22385b59552e25a",662   "language": "R",663   "lines": 27,664   "truncated": false,665   "block": 1,666   "row": 10021667  },668  {669   "path": "R/CSIDE_utils.R",670   "sha256": "0fd838d4c2097eb56b96d092082ee22e418918c891b74e33867013b7e98c8711",671   "language": "R",672   "lines": 467,673   "truncated": false,674   "block": 1,675   "row": 10568676  },677  {678   "path": "R/IRWLS.R",679   "sha256": "e5a1687cc39e7a6dd512914133d058c891a7aea641baa19ac3a13b38a1670094",680   "language": "R",681   "lines": 106,682   "truncated": false,683   "block": 1,684   "row": 10194685  },686  {687   "path": "R/RCTD_helper.R",688   "sha256": "550efaf30f1df94be2d8795e3bae5877ae959e19f469dbc905e18abba1e636cf",689   "language": "R",690   "lines": 235,691   "truncated": false,692   "block": 1,693   "row": 10466694  },695  {696   "path": "R/RCTDreplicates.R",697   "sha256": "7715e5ad9a6b9b46ebf9f2140e97c73e10a72172ca1ebb9acf74be7ac97b4eb8",698   "language": "R",699   "lines": 308,700   "truncated": false,701   "block": 1,702   "row": 10570703  },704  {705   "path": "R/Reference.R",706   "sha256": "81f69532600565404955bb19801c6c55d42aae68e27a0b788ba7024fe4c34807",707   "language": "R",708   "lines": 118,709   "truncated": false,710   "block": 1,711   "row": 10319712  },713  {714   "path": "R/SpatialRNA.R",715   "sha256": "7c5fe064159a2b28f57f2e174ad697bfa0ba53e56801fa9e647a321324955e45",716   "language": "R",717   "lines": 236,718   "truncated": false,719   "block": 1,720   "row": 10461721  },722  {723   "path": "R/classes.R",724   "sha256": "e9279ff79cb3d44f43ac122e56d763c4b338d5a0fa316a6a9eb5a46f9db2b55f",725   "language": "R",726   "lines": 172,727   "truncated": false,728   "block": 1,729   "row": 10359730  },731  {732   "path": "R/platform_effect_normalization.R",733   "sha256": "792129b755a3d549a40f9eafe461fa69ea99d1da9b0abaef9bbfcbbcb774e421",734   "language": "R",735   "lines": 109,736   "truncated": false,737   "block": 1,738   "row": 10302739  },740  {741   "path": "R/plotting.R",742   "sha256": "6dadefedbfccc05cd33963941d4ca85be6ca56ffbbc4cd2dc1eefcae24489972",743   "language": "R",744   "lines": 449,745   "truncated": false,746   "block": 1,747   "row": 10559748  },749  {750   "path": "R/postProcessing.R",751   "sha256": "0ee4a1350a25d6598dd5d7448b863c02dd9a6d2009f287188bb76950f2ef93c2",752   "language": "R",753   "lines": 137,754   "truncated": false,755   "block": 1,756   "row": 10358757  },758  {759   "path": "R/prob_model.R",760   "sha256": "dfb0a9aaec66e4398f5cdb1075f21cc0a0a1ee6db14b9719cf048a74c0aa2e20",761   "language": "R",762   "lines": 209,763   "truncated": false,764   "block": 1,765   "row": 10339766  },767  {768   "path": "R/processRef.R",769   "sha256": "3237305e2136f9b529777d2fe05136b4a2db9fefb093ff3fbb786f0cb93593b6",770   "language": "R",771   "lines": 59,772   "truncated": false,773   "block": 1,774   "row": 10147775  },776  {777   "path": "R/replintegrate.R",778   "sha256": "53ee829241f6613a5529b1d6b5384cc2c219f1c5e4c2542f1a0203e3b9408b72",779   "language": "R",780   "lines": 59,781   "truncated": false,782   "block": 1,783   "row": 10101784  },785  {786   "path": "R/repliterate.R",787   "sha256": "aa5e2ed8204cbf4d4b75823cb072f5ca5673d81e338bc97182844268b83d9746",788   "language": "R",789   "lines": 30,790   "truncated": false,791   "block": 1,792   "row": 9992793  },794  {795   "path": "R/runRCTD.R",796   "sha256": "818e086dd1fc02ab19d52ca9143375228038af30d5f9715d7ea1dfbac2848f76",797   "language": "R",798   "lines": 204,799   "truncated": false,800   "block": 1,801   "row": 10465802  },803  {804   "path": "R/spacexr.R",805   "sha256": "630e46cbb6c8915f4dd0e9234fa6d0ae2c5c35b9338c990e6911062625d7eff8",806   "language": "R",807   "lines": 165,808   "truncated": false,809   "block": 1,810   "row": 10447811  },812  {813   "path": "R/utils.R",814   "sha256": "775e068720defd167d220013e6ba5f5e9f5f8e21867603d2c7c6861da31858a3",815   "language": "R",816   "lines": 131,817   "truncated": false,818   "block": 1,819   "row": 10314820  },821  {822   "path": "README.Rmd",823   "sha256": "0332013420eb973bf1c525857a17cec3f935ec9b4bc6952a6d0fbe976833b333",824   "language": "R",825   "lines": 148,826   "truncated": false,827   "block": 1,828   "row": 10497829  },830  {831   "path": "README.md",832   "sha256": "a3476273556ca4e7e532c8c059cadffb0ca77817dc5521b2a1398dbba32b020f",833   "language": "Text",834   "lines": 288,835   "truncated": false,836   "block": 1,837   "row": 11982838  },839  {840   "path": "documentation/README.Rmd",841   "sha256": "e679f66d3a0eed138c63f2ba08c285cf6f4a6b203356e1213cd67160aac38e0c",842   "language": "R",843   "lines": 243,844   "truncated": false,845   "block": 1,846   "row": 10551847  },848  {849   "path": "vignettes/CSIDE_celltocell_interactions.Rmd",850   "sha256": "8ae5640b349df1e00c55fb4634d2fd58bafab0741a8efe920efe7a3eaa2620ef",851   "language": "R",852   "lines": 155,853   "truncated": false,854   "block": 1,855   "row": 10371856  },857  {858   "path": "vignettes/CSIDE_pathology_interactions.Rmd",859   "sha256": "af32061e57f8000f0f4302509a05f95dbb435aebd37cf57bd72c8c2999c30027",860   "language": "R",861   "lines": 154,862   "truncated": false,863   "block": 1,864   "row": 10379865  },866  {867   "path": "vignettes/CSIDE_two_regions.Rmd",868   "sha256": "e51fb6b1de696a240eff732be1766ee918cc3276ce0f86f565232c9b09ca9172",869   "language": "R",870   "lines": 157,871   "truncated": false,872   "block": 1,873   "row": 10376874  },875  {876   "path": "vignettes/README.Rmd",877   "sha256": "7765b1369435cbc44be7b3445469f6b95f37d054ae878c098497c104ff1640d0",878   "language": "R",879   "lines": 63,880   "truncated": false,881   "block": 1,882   "row": 10239883  },884  {885   "path": "vignettes/differential-expression.Rmd",886   "sha256": "7a075d5866fc01d3e21ade0e1320458fddd5c50e05730d59a1bb5c5e6ac642b8",887   "language": "R",888   "lines": 143,889   "truncated": false,890   "block": 1,891   "row": 10355892  },893  {894   "path": "vignettes/merfish_nonparametric.Rmd",895   "sha256": "9bb3401fe4614ad4211731799e79c8c9c3e1664e048812650d5ba2ad41ff21b6",896   "language": "R",897   "lines": 140,898   "truncated": false,899   "block": 1,900   "row": 10367901  },902  {903   "path": "vignettes/replicates.Rmd",904   "sha256": "ebd44df9233be9916ed4a58ea27f90baca3d91e2d757f7a95efe6de669422d11",905   "language": "R",906   "lines": 188,907   "truncated": false,908   "block": 1,909   "row": 10470910  },911  {912   "path": "vignettes/spatial-transcriptomics.Rmd",913   "sha256": "b92da990f1246477a6f8bb8b45f02c2425ac47adb764751f458b846caa75d26f",914   "language": "R",915   "lines": 183,916   "truncated": false,917   "block": 1,918   "row": 10448919  },920  {921   "path": "vignettes/visium_CSIDE_celltocell_interactions.Rmd",922   "sha256": "280c6281fe69fcb11ae02d1993eb09eb72fa1c3c842bf549b98e1bef9a0d2c40",923   "language": "R",924   "lines": 86,925   "truncated": false,926   "block": 1,927   "row": 10216928  },929  {930   "path": "vignettes/visium_full_regions.Rmd",931   "sha256": "78d2fc36e5fb68ea7cd220d140bb1dbd3ff99f1289372965eb8ee2ec31eed07b",932   "language": "R",933   "lines": 178,934   "truncated": false,935   "block": 1,936   "row": 10410937  },938  {939   "path": "vignettes/visium_multi.Rmd",940   "sha256": "96930c9de093d8f8544a54123d727fca27d0b47ec0d1820044a32a9f54682f27",941   "language": "R",942   "lines": 91,943   "truncated": false,944   "block": 1,945   "row": 10224946  }947 ]948}