{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":508785204,"defaultBranch":"main","name":"phenotypic_profiling","ownerLogin":"WayScience","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2022-06-29T17:25:47.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/88446464?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1726520910.0","currentOid":""},"activityList":{"items":[{"before":"7aa47ba1a05d82524ea3ecd93e1abfb3c56bf960","after":"92e4025d83b556194ebabf5d71f598b9b66a12a7","ref":"refs/heads/main","pushedAt":"2024-09-16T18:11:03.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"gwaybio","name":"Gregory Way","path":"/gwaybio","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7340421?s=80&v=4"},"commit":{"message":"[Response to Reviewers] Add Silhouette analysis (#68)\n\n* add notebook and results for silhouette scores\r\n\r\n* add silhouette visualization\r\n\r\n* calculate total silhouette sum per feature space\r\n\r\n* remove unused file name reference","shortMessageHtmlLink":"[Response to Reviewers] Add Silhouette analysis (#68)"}},{"before":"19bb76440cc42a213986e20d6d1e37056b7b37ac","after":"7aa47ba1a05d82524ea3ecd93e1abfb3c56bf960","ref":"refs/heads/main","pushedAt":"2024-09-16T18:02:34.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"gwaybio","name":"Gregory Way","path":"/gwaybio","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7340421?s=80&v=4"},"commit":{"message":"[Response to Reviewers] Update dimensionality reduction figures (#67)\n\n* fix argument and path\r\n\r\n* move faceted UMAP to panel A\r\n\r\n* update supplementary umap after updating umap in fig2\r\n\r\n* add tsne figure notebooks\r\n\r\n* add notebook for applying tsne\r\n\r\n* fix typo and rerun notebook\r\n\r\n* respond to reviewer comments\r\n\r\n* remove unused variables and make tsv","shortMessageHtmlLink":"[Response to Reviewers] Update dimensionality reduction figures (#67)"}},{"before":"a8d4e142e427544ceffc143ff42299101548a629","after":"19bb76440cc42a213986e20d6d1e37056b7b37ac","ref":"refs/heads/main","pushedAt":"2024-03-13T18:21:34.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"gwaybio","name":"Gregory Way","path":"/gwaybio","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7340421?s=80&v=4"},"commit":{"message":"Update README.md","shortMessageHtmlLink":"Update README.md"}},{"before":"17c017439b07d5530b9373748d93c7e6b3f3e9c2","after":"a8d4e142e427544ceffc143ff42299101548a629","ref":"refs/heads/main","pushedAt":"2024-03-12T15:54:38.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"gwaybio","name":"Gregory Way","path":"/gwaybio","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7340421?s=80&v=4"},"commit":{"message":"increase size of fig 4 (#66)","shortMessageHtmlLink":"increase size of fig 4 (#66)"}},{"before":"cb4883b88e6b6bc29ac8c9d98875dd179c1684c8","after":"17c017439b07d5530b9373748d93c7e6b3f3e9c2","ref":"refs/heads/main","pushedAt":"2024-03-08T19:36:45.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"gwaybio","name":"Gregory Way","path":"/gwaybio","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7340421?s=80&v=4"},"commit":{"message":"Switch to top 100 enriched treatments in JUMP (new sup table) (#60)\n\n* switch to top 100 instead of top 10\r\n\r\n* rerun processing and update .gz files\r\n\r\n* rerun notebook and minor mods","shortMessageHtmlLink":"Switch to top 100 enriched treatments in JUMP (new sup table) (#60)"}},{"before":"18488dde58ae55f5cb4c9b7588834b8c5c660bcc","after":"cb4883b88e6b6bc29ac8c9d98875dd179c1684c8","ref":"refs/heads/main","pushedAt":"2024-03-08T13:28:06.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"gwaybio","name":"Gregory Way","path":"/gwaybio","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7340421?s=80&v=4"},"commit":{"message":"update download path (#65)","shortMessageHtmlLink":"update download path (#65)"}},{"before":"68642054ca46d1a7a4efd825222a218598e22a20","after":"18488dde58ae55f5cb4c9b7588834b8c5c660bcc","ref":"refs/heads/main","pushedAt":"2024-03-08T13:03:04.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"gwaybio","name":"Gregory Way","path":"/gwaybio","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7340421?s=80&v=4"},"commit":{"message":"Add JUMP analysis figure (#55)\n\n* add first two panels of JUMP figure\r\n\r\n* add sup fig 9\r\n\r\n* add updated figures\r\n\r\n* remove phenotype profile umap\r\n\r\n* add/remove jump processed files\r\n\r\n* finalize figure 5\r\n\r\n* response to review","shortMessageHtmlLink":"Add JUMP analysis figure (#55)"}},{"before":"f99d92e069d2e6aaef238f553781a20546871983","after":"68642054ca46d1a7a4efd825222a218598e22a20","ref":"refs/heads/main","pushedAt":"2024-03-08T12:45:34.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"gwaybio","name":"Gregory Way","path":"/gwaybio","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7340421?s=80&v=4"},"commit":{"message":"Minor tweaks to Sup Figure 8 (#59)\n\n* update sup fig 8\r\n\r\n* response to review","shortMessageHtmlLink":"Minor tweaks to Sup Figure 8 (#59)"}},{"before":"bb49045701dd96b96f60c2dca5cf7cef4c2432fe","after":"f99d92e069d2e6aaef238f553781a20546871983","ref":"refs/heads/main","pushedAt":"2024-03-08T12:17:31.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"gwaybio","name":"Gregory Way","path":"/gwaybio","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7340421?s=80&v=4"},"commit":{"message":"minor tweaks to sup fig 7 (#58)","shortMessageHtmlLink":"minor tweaks to sup fig 7 (#58)"}},{"before":"08a3e8d297ca046222ce90e29d2958f2d38569f2","after":"bb49045701dd96b96f60c2dca5cf7cef4c2432fe","ref":"refs/heads/main","pushedAt":"2024-03-06T15:29:23.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"gwaybio","name":"Gregory Way","path":"/gwaybio","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7340421?s=80&v=4"},"commit":{"message":"Add details to Readme (#64)","shortMessageHtmlLink":"Add details to Readme (#64)"}},{"before":"84875352cb6f3fd6f738fc1c77b17ae7791e1163","after":"08a3e8d297ca046222ce90e29d2958f2d38569f2","ref":"refs/heads/main","pushedAt":"2024-03-05T00:32:07.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"roshankern","name":"Roshan Kern","path":"/roshankern","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/105665675?s=80&v=4"},"commit":{"message":"Repo cleanup (#62)\n\n* main readme\r\n\r\n* download data\r\n\r\n* split data\r\n\r\n* train model readme\r\n\r\n* evaluate\r\n\r\n* interpret model\r\n\r\n* validate model\r\n\r\n* single cell images\r\n\r\n* Update 2.train_model/README.md\r\n\r\nCo-authored-by: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com>\r\n\r\n* Update 5.validate_model/README.md\r\n\r\nCo-authored-by: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com>\r\n\r\n* Update 2.train_model/README.md\r\n\r\nCo-authored-by: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com>\r\n\r\n* Update README.md\r\n\r\nCo-authored-by: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com>\r\n\r\n* Update README.md\r\n\r\nCo-authored-by: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com>\r\n\r\n* Update README.md\r\n\r\nCo-authored-by: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com>\r\n\r\n---------\r\n\r\nCo-authored-by: Gregory Way \r\nCo-authored-by: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com>","shortMessageHtmlLink":"Repo cleanup (#62)"}},{"before":"b40e626b20581e19b4c22c15325f7a7cfcc65777","after":"84875352cb6f3fd6f738fc1c77b17ae7791e1163","ref":"refs/heads/main","pushedAt":"2024-03-04T18:21:13.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"gwaybio","name":"Gregory Way","path":"/gwaybio","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7340421?s=80&v=4"},"commit":{"message":"Add enrichment and introductory notes to readme (#61)","shortMessageHtmlLink":"Add enrichment and introductory notes to readme (#61)"}},{"before":"4718b0793656d3df4787a50d78626f6d49dbcb56","after":"b40e626b20581e19b4c22c15325f7a7cfcc65777","ref":"refs/heads/main","pushedAt":"2024-02-21T13:32:12.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"gwaybio","name":"Gregory Way","path":"/gwaybio","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7340421?s=80&v=4"},"commit":{"message":"Process jump single cell data (#56)\n\n* add parquet support to env\r\n\r\n* add notebook to process jump phenotype profiles\r\n\r\n* add jump results and profiles\r\n\r\n* integrate extended jump metadata\r\n\r\n* add updated jump results\r\n\r\n* add umap\r\n\r\n* add umap coordinates and update other files after rerunning\r\n\r\n* add umap to env\r\n\r\n* response to PR comments\r\n\r\n* rerun notebook to update jump datasets\r\n\r\nalso add comparison across cell types","shortMessageHtmlLink":"Process jump single cell data (#56)"}},{"before":"14130313eddd350182d61374943a897503c74f38","after":"4718b0793656d3df4787a50d78626f6d49dbcb56","ref":"refs/heads/main","pushedAt":"2024-02-14T23:40:13.000Z","pushType":"pr_merge","commitsCount":8,"pusher":{"login":"jenna-tomkinson","name":"Jenna Tomkinson","path":"/jenna-tomkinson","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/107513215?s=80&v=4"},"commit":{"message":"Merge pull request #57 from jenna-tomkinson/figure1\n\nAdd Figure 1","shortMessageHtmlLink":"Merge pull request #57 from jenna-tomkinson/figure1"}},{"before":"e62dedfebec3b7089858fadf3c77f065dbb0f1d2","after":"14130313eddd350182d61374943a897503c74f38","ref":"refs/heads/main","pushedAt":"2024-02-09T12:44:15.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"gwaybio","name":"Gregory Way","path":"/gwaybio","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7340421?s=80&v=4"},"commit":{"message":"Adding feature importance visualizations (#48)\n\n* select colors for CP feature groups\r\n\r\n* add magick to environment\r\n\r\n* add notebook to generate feature importance heatmaps\r\n\r\n* update heatmaps based on pr comments","shortMessageHtmlLink":"Adding feature importance visualizations (#48)"}},{"before":"d04510115abe7bd7f3d596c3727819fa341b3bcf","after":"e62dedfebec3b7089858fadf3c77f065dbb0f1d2","ref":"refs/heads/main","pushedAt":"2024-02-06T13:32:49.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"gwaybio","name":"Gregory Way","path":"/gwaybio","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7340421?s=80&v=4"},"commit":{"message":"add supplementary LOIO figure (#53)","shortMessageHtmlLink":"add supplementary LOIO figure (#53)"}},{"before":"2b973506e721aed352827e7fb33d6b597743d430","after":"d04510115abe7bd7f3d596c3727819fa341b3bcf","ref":"refs/heads/main","pushedAt":"2024-02-06T02:58:42.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"gwaybio","name":"Gregory Way","path":"/gwaybio","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7340421?s=80&v=4"},"commit":{"message":"Updating LOIO visualization (#47)\n\n* update summary notebook of LOIO analysis\r\n\r\n* update LOIO analysis to include all feature spaces\r\n\r\n* update LOIO evaluation with no-ic run\r\n\r\n* delete legacy LOIO summary files\r\n\r\n* add updated summary rank files after no-ic\r\n\r\n* fix comment re. pr review\r\n\r\n* fix colors to show boxplot median\r\n\r\n* update figure 4 with new LOIO analysis and in response to PR comments\r\n\r\n* remove panel a, belong in methods\r\n\r\n* add clarifying comment about the model we visualize","shortMessageHtmlLink":"Updating LOIO visualization (#47)"}},{"before":"bd40d5ff36b09aad4babbb428f6cd9a714956524","after":null,"ref":"refs/heads/use-no-ic","pushedAt":"2024-02-03T15:53:35.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"roshankern","name":"Roshan Kern","path":"/roshankern","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/105665675?s=80&v=4"}},{"before":"90662250af72a8b40acf43dbab190c41542ce0e9","after":"2b973506e721aed352827e7fb33d6b597743d430","ref":"refs/heads/main","pushedAt":"2024-02-03T15:53:24.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"roshankern","name":"Roshan Kern","path":"/roshankern","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/105665675?s=80&v=4"},"commit":{"message":"Add models with no-ic [training and LOIO] (#51)\n\n* Add No IC (0.Download, 1.Split, 2.Train) (#49)\r\n\r\n* update download module\r\n\r\n* rename saved labeled data\r\n\r\n* update split data module\r\n\r\n* add new train models script\r\n\r\n* update readmes\r\n\r\n* update running model code\r\n\r\n* update get x y function\r\n\r\n* mike suggestions\r\n\r\n* add new models\r\n\r\n* Update evaluate module (no ic) (#50)\r\n\r\n* update evaluate module\r\n\r\n* update scripts\r\n\r\n* add documentation\r\n\r\n* documentation\r\n\r\n* remove unecessary notebook\r\n\r\n* Update 3.evaluate_model/README.md\r\n\r\nCo-authored-by: Gregory Way \r\n\r\n* add comment\r\n\r\n---------\r\n\r\nCo-authored-by: Gregory Way \r\n\r\n* rerun LOIO with no-ic\r\n\r\n* add no-ic results as lfs file\r\n\r\n* define test ratio\r\n\r\n* update docs\r\n\r\n* rename probabilities file\r\n\r\n* fix typo in file name\r\n\r\n* move file names and fix attributes file\r\n\r\n* add fixed file name\r\n\r\n* update download module\r\n\r\n---------\r\n\r\nCo-authored-by: Roshan Kern <105665675+roshankern@users.noreply.github.com>\r\nCo-authored-by: roshankern ","shortMessageHtmlLink":"Add models with no-ic [training and LOIO] (#51)"}},{"before":"49d74f5f91b402e432142577331fbce552cb427e","after":"bd40d5ff36b09aad4babbb428f6cd9a714956524","ref":"refs/heads/use-no-ic","pushedAt":"2024-02-03T15:50:20.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"roshankern","name":"Roshan Kern","path":"/roshankern","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/105665675?s=80&v=4"},"commit":{"message":"update download module","shortMessageHtmlLink":"update download module"}},{"before":"46c1ee969c6565924f1dd39de392d874cd78a788","after":"49d74f5f91b402e432142577331fbce552cb427e","ref":"refs/heads/use-no-ic","pushedAt":"2024-01-30T13:17:07.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"gwaybio","name":"Gregory Way","path":"/gwaybio","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7340421?s=80&v=4"},"commit":{"message":"add fixed file name","shortMessageHtmlLink":"add fixed file name"}},{"before":"36738b24eb0c3d53ece3fd3711a19b0bb74df3d6","after":"46c1ee969c6565924f1dd39de392d874cd78a788","ref":"refs/heads/use-no-ic","pushedAt":"2024-01-30T13:16:39.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"gwaybio","name":"Gregory Way","path":"/gwaybio","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7340421?s=80&v=4"},"commit":{"message":"move file names and fix attributes file","shortMessageHtmlLink":"move file names and fix attributes file"}},{"before":"5884f4cc150192c07b4325ba2d14d3b650ef6610","after":"36738b24eb0c3d53ece3fd3711a19b0bb74df3d6","ref":"refs/heads/use-no-ic","pushedAt":"2024-01-30T13:14:18.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"gwaybio","name":"Gregory Way","path":"/gwaybio","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7340421?s=80&v=4"},"commit":{"message":"fix typo in file name","shortMessageHtmlLink":"fix typo in file name"}},{"before":"dd86d062d0877bca9c67079ece9fc0655a08a362","after":"5884f4cc150192c07b4325ba2d14d3b650ef6610","ref":"refs/heads/use-no-ic","pushedAt":"2024-01-29T15:53:41.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"roshankern","name":"Roshan Kern","path":"/roshankern","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/105665675?s=80&v=4"},"commit":{"message":"update docs","shortMessageHtmlLink":"update docs"}},{"before":"f86dad1a1ba339202c839b6554184131aa1d0b2d","after":"dd86d062d0877bca9c67079ece9fc0655a08a362","ref":"refs/heads/use-no-ic","pushedAt":"2024-01-29T15:45:11.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"roshankern","name":"Roshan Kern","path":"/roshankern","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/105665675?s=80&v=4"},"commit":{"message":"define test ratio","shortMessageHtmlLink":"define test ratio"}},{"before":"a6909edcb8d4899a7ce0f7875478641e2f644e3a","after":"f86dad1a1ba339202c839b6554184131aa1d0b2d","ref":"refs/heads/use-no-ic","pushedAt":"2024-01-28T20:57:31.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"gwaybio","name":"Gregory Way","path":"/gwaybio","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7340421?s=80&v=4"},"commit":{"message":"add no-ic results as lfs file","shortMessageHtmlLink":"add no-ic results as lfs file"}},{"before":"1fdf5ce4fa15ac6863ed6c72d02053d23f37c869","after":"a6909edcb8d4899a7ce0f7875478641e2f644e3a","ref":"refs/heads/use-no-ic","pushedAt":"2024-01-28T20:54:30.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"gwaybio","name":"Gregory Way","path":"/gwaybio","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7340421?s=80&v=4"},"commit":{"message":"rerun LOIO with no-ic","shortMessageHtmlLink":"rerun LOIO with no-ic"}},{"before":"415710f6f31c4aabf0e1d2912ed773882da6140b","after":"1fdf5ce4fa15ac6863ed6c72d02053d23f37c869","ref":"refs/heads/use-no-ic","pushedAt":"2024-01-22T17:27:26.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"roshankern","name":"Roshan Kern","path":"/roshankern","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/105665675?s=80&v=4"},"commit":{"message":"Update evaluate module (no ic) (#50)\n\n* update evaluate module\r\n\r\n* update scripts\r\n\r\n* add documentation\r\n\r\n* documentation\r\n\r\n* remove unecessary notebook\r\n\r\n* Update 3.evaluate_model/README.md\r\n\r\nCo-authored-by: Gregory Way \r\n\r\n* add comment\r\n\r\n---------\r\n\r\nCo-authored-by: Gregory Way ","shortMessageHtmlLink":"Update evaluate module (no ic) (#50)"}},{"before":"60b8c61ae92fed380b2e902b32e1898c67390dde","after":null,"ref":"refs/heads/add-no-ic","pushedAt":"2024-01-22T15:52:37.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"roshankern","name":"Roshan Kern","path":"/roshankern","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/105665675?s=80&v=4"}},{"before":null,"after":"60b8c61ae92fed380b2e902b32e1898c67390dde","ref":"refs/heads/add-no-ic","pushedAt":"2024-01-22T15:51:46.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"roshankern","name":"Roshan Kern","path":"/roshankern","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/105665675?s=80&v=4"},"commit":{"message":"add new models","shortMessageHtmlLink":"add new models"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"Y3Vyc29yOnYyOpK7MjAyNC0wOS0xNlQxODoxMTowMy4wMDAwMDBazwAAAAS3vfvC","startCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wOS0xNlQxODoxMTowMy4wMDAwMDBazwAAAAS3vfvC","endCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wMS0yMlQxNTo1MTo0Ni4wMDAwMDBazwAAAAPmAbgY"}},"title":"Activity ยท WayScience/phenotypic_profiling"}