{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":182295433,"defaultBranch":"master","name":"profiling-resistance-mechanisms","ownerLogin":"broadinstitute","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2019-04-19T16:37:08.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/393552?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1689889241.0","currentOid":""},"activityList":{"items":[{"before":"a52908408e2ac2b428894760914837eae97b43a4","after":"7d160b119b159a06f76c717c2c3a26c9868e8842","ref":"refs/heads/master","pushedAt":"2023-10-03T16:09:49.000Z","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":"e10a4ace5b7973fc74280f0a7b9bb99f5fc17b42","after":"a52908408e2ac2b428894760914837eae97b43a4","ref":"refs/heads/master","pushedAt":"2023-07-20T21:45:23.000Z","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":"11e711fd8241ef5a4fc4a6c4c13b21eea74bbb94","after":"e10a4ace5b7973fc74280f0a7b9bb99f5fc17b42","ref":"refs/heads/master","pushedAt":"2023-07-19T12:12:59.000Z","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":"Make clone labels consistent (#133)\n\n* recode names of some clones that were inconsistent\r\n\r\n* update ks test between misclassified samples\r\n\r\n* recreate figure with updated clone labels\r\n\r\nother minor tweaks\r\n\r\n* restrict figure to only those clones used in the paper","shortMessageHtmlLink":"Make clone labels consistent (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"1810575842\" data-permission-text=\"Title is private\" data-url=\"https://github.com/broadinstitute/profiling-resistance-mechanisms/issues/133\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/broadinstitute/profiling-resistance-mechanisms/pull/133/hovercard\" href=\"https://github.com/broadinstitute/profiling-resistance-mechanisms/pull/133\">#133</a>)"}},{"before":"90b9b6228603338214047a90387a5ec5424cf32d","after":"11e711fd8241ef5a4fc4a6c4c13b21eea74bbb94","ref":"refs/heads/master","pushedAt":"2023-07-18T18:37:36.000Z","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] Replace \"all except bz\" features with \"random\" features (#132)\n\n* replace all except bz features with random\r\n\r\n* fix facet","shortMessageHtmlLink":"[Response to Reviewers] Replace \"all except bz\" features with \"random…"}},{"before":"49dbca43556d2789afc1339096fea97ee625b41f","after":"90b9b6228603338214047a90387a5ec5424cf32d","ref":"refs/heads/master","pushedAt":"2023-07-14T18:11:59.000Z","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 signature summary visualization (#131)","shortMessageHtmlLink":"add signature summary visualization (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"1805301310\" data-permission-text=\"Title is private\" data-url=\"https://github.com/broadinstitute/profiling-resistance-mechanisms/issues/131\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/broadinstitute/profiling-resistance-mechanisms/pull/131/hovercard\" href=\"https://github.com/broadinstitute/profiling-resistance-mechanisms/pull/131\">#131</a>)"}},{"before":"e615978f068cfb207707717e9359a932e80b59e0","after":"49dbca43556d2789afc1339096fea97ee625b41f","ref":"refs/heads/master","pushedAt":"2023-07-14T15:28:56.000Z","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] Adding analysis and visualization of misclassified samples (#130)\n\n* add notebook to summarize accuracy per sample category\r\n\r\n* perform ks test against misclassified samples and high confident samples\r\n\r\n* add visualization of the sample misclassification analysis\r\n\r\n* update axis text","shortMessageHtmlLink":"[Response to Reviewers] Adding analysis and visualization of misclass…"}},{"before":"0ab5ea1789d45640659b4871cd1c21824ef0c064","after":"e615978f068cfb207707717e9359a932e80b59e0","ref":"refs/heads/master","pushedAt":"2023-07-13T19:39:36.000Z","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] Make feature space consistent size with PCA and plot multiple metrics (#129)\n\n* use 30 principal components\r\n\r\nto make the comparisons equal in feature count\r\n\r\n* update visualization for 30 pcs\r\n\r\nalso viz three metrics","shortMessageHtmlLink":"[Response to Reviewers] Make feature space consistent size with PCA a…"}},{"before":"56fd4d7432f3128b24d4b0056d297b0f72c74e8f","after":"0ab5ea1789d45640659b4871cd1c21824ef0c064","ref":"refs/heads/master","pushedAt":"2023-07-13T17:46:20.000Z","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 feature space analysis (UMAP and clustering) (#128)\n\n* output profiles prior to feature selection\r\n\r\n* add figure environment\r\n\r\n* calculate umap coordinates for each feature space\r\n\r\n* add notebook to create umap figure\r\n\r\n* add signature exploration environment\r\n\r\n* add supplementary umap figure\r\n\r\n* add umap coordinates\r\n\r\n* remove new line character\r\n\r\n* add clustering analysis and rename notebook\r\n\r\n* add visualization of clustering results and rename\r\n\r\n* add patchwork\r\n\r\n* add results and viz","shortMessageHtmlLink":"[Response to Reviewers] Add feature space analysis (UMAP and clusteri…"}},{"before":"90548105bb3bea5bf9b88c186fa4125848002991","after":"56fd4d7432f3128b24d4b0056d297b0f72c74e8f","ref":"refs/heads/master","pushedAt":"2023-07-11T20:10:02.000Z","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 files relevant to figure generation (#125)\n\n* testing ability to add files to mekelley branch\r\n\r\n* adding test file to check abilities\r\n\r\n* adding readmes and files relevant to figure generation\r\n\r\nTrying to add relevant files for figure generation (prism, matlab, csv, md files)\r\n\r\nNOTE: one file (prism volcanos file) was over 100 MB and too large to be pushed. How should I add this to the repo?\r\n\r\nAdding Greg to make sure this push worked and makes sense\r\n\r\nCo-Authored-By: Gregory Way <gregory.way@gmail.com>\r\n\r\n* Reformat READMEs\r\n\r\nREADMEs reformatted to have one sentence per line\r\n\r\n* add volcanos.pzfx\r\n\r\n* recommit figure generating code/files\r\n\r\nrecommitting figure generating code to remove csv files but keep UNIQUE files\r\n\r\n* remove csv files\r\n\r\n---------\r\n\r\nCo-authored-by: Gregory Way <gregory.way@gmail.com>","shortMessageHtmlLink":"Adding files relevant to figure generation (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"1527957956\" data-permission-text=\"Title is private\" data-url=\"https://github.com/broadinstitute/profiling-resistance-mechanisms/issues/125\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/broadinstitute/profiling-resistance-mechanisms/pull/125/hovercard\" href=\"https://github.com/broadinstitute/profiling-resistance-mechanisms/pull/125\">#125</a>)"}},{"before":"f48cf998aeedf41165f3081e11c821ac0756d37c","after":"694e7e9c6b5df8be3fab632d4f407e078daa09d5","ref":"refs/heads/cpg-upload","pushedAt":"2023-06-28T14:58:21.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"shntnu","name":"Shantanu Singh","path":"/shntnu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1210428?s=80&v=4"},"commit":{"message":"Update cpg_upload.sh","shortMessageHtmlLink":"Update cpg_upload.sh"}},{"before":"183e93826093fe0cca2a16b8fbc808c1992dd0a6","after":"f48cf998aeedf41165f3081e11c821ac0756d37c","ref":"refs/heads/cpg-upload","pushedAt":"2023-06-28T14:54:49.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"shntnu","name":"Shantanu Singh","path":"/shntnu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1210428?s=80&v=4"},"commit":{"message":"Update cpg_upload.sh","shortMessageHtmlLink":"Update cpg_upload.sh"}},{"before":"8422a0a44efd088fa6d629b15e5241b87072ddfe","after":"183e93826093fe0cca2a16b8fbc808c1992dd0a6","ref":"refs/heads/cpg-upload","pushedAt":"2023-06-28T14:51:41.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"shntnu","name":"Shantanu Singh","path":"/shntnu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1210428?s=80&v=4"},"commit":{"message":"Update cpg_upload.sh","shortMessageHtmlLink":"Update cpg_upload.sh"}},{"before":"95e298a3ff26fb4611e23fec2eb387a84c30fdd4","after":"8422a0a44efd088fa6d629b15e5241b87072ddfe","ref":"refs/heads/cpg-upload","pushedAt":"2023-06-28T14:50:00.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"shntnu","name":"Shantanu Singh","path":"/shntnu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1210428?s=80&v=4"},"commit":{"message":"Update cpg_upload.sh","shortMessageHtmlLink":"Update cpg_upload.sh"}},{"before":"e3f0d5ee8c2353e1c317522397456ee316b501db","after":"95e298a3ff26fb4611e23fec2eb387a84c30fdd4","ref":"refs/heads/cpg-upload","pushedAt":"2023-06-28T14:49:08.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"shntnu","name":"Shantanu Singh","path":"/shntnu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1210428?s=80&v=4"},"commit":{"message":"Update cpg_upload.sh","shortMessageHtmlLink":"Update cpg_upload.sh"}},{"before":null,"after":"e3f0d5ee8c2353e1c317522397456ee316b501db","ref":"refs/heads/cpg-upload","pushedAt":"2023-06-28T14:44:30.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"shntnu","name":"Shantanu Singh","path":"/shntnu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1210428?s=80&v=4"},"commit":{"message":"Create cpg_upload.sh","shortMessageHtmlLink":"Create cpg_upload.sh"}},{"before":"9bc5d4ccdc81fc978354d3e532a899ba6266959d","after":"90548105bb3bea5bf9b88c186fa4125848002991","ref":"refs/heads/master","pushedAt":"2023-04-05T22:11:20.000Z","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":"adding zenodo doi","shortMessageHtmlLink":"adding zenodo doi"}}],"hasNextPage":false,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAADjnnrnwA","startCursor":null,"endCursor":null}},"title":"Activity · broadinstitute/profiling-resistance-mechanisms"}