{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":761228425,"defaultBranch":"devel","name":"HoloFoodR","ownerLogin":"EBI-Metagenomics","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2024-02-21T13:34:54.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/32897658?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1719510597.0","currentOid":""},"activityList":{"items":[{"before":"b28072c8336ecbc7e373e72323ea85eb60997257","after":"3f6d33e3c394aeee752deabfb4814f5db2fbd238","ref":"refs/heads/gh-pages","pushedAt":"2024-06-27T18:02:53.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"github-actions[bot]","name":null,"path":"/apps/github-actions","primaryAvatarUrl":"https://avatars.githubusercontent.com/in/15368?s=80&v=4"},"commit":{"message":"Deploying to gh-pages from @ EBI-Metagenomics/HoloFoodR@815071128cdd8e099fbee032dd56fc12a14bfd00 🚀","shortMessageHtmlLink":"Deploying to gh-pages from @ <a class=\"commit-link\" data-hovercard-type=\"commit\" data-hovercard-url=\"https://github.com/EBI-Metagenomics/HoloFoodR/commit/815071128cdd8e099fbee032dd56fc12a14bfd00/hovercard\" href=\"https://github.com/EBI-Metagenomics/HoloFoodR/commit/815071128cdd8e099fbee032dd56fc12a14bfd00\"><tt>8150711</tt></a> 🚀"}},{"before":"fc5c0e5c1ff93c2a04585769ab73e64268bcc4be","after":null,"ref":"refs/heads/fixes","pushedAt":"2024-06-27T17:49:57.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"TuomasBorman","name":"Tuomas Borman","path":"/TuomasBorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/60338854?s=80&v=4"}},{"before":"737983440ce72b6b7af5d16c52c92f991c078a38","after":"815071128cdd8e099fbee032dd56fc12a14bfd00","ref":"refs/heads/devel","pushedAt":"2024-06-27T17:49:54.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"TuomasBorman","name":"Tuomas Borman","path":"/TuomasBorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/60338854?s=80&v=4"},"commit":{"message":"Minor fixes to documentation (#29)","shortMessageHtmlLink":"Minor fixes to documentation (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2378711437\" data-permission-text=\"Title is private\" data-url=\"https://github.com/EBI-Metagenomics/HoloFoodR/issues/29\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/EBI-Metagenomics/HoloFoodR/pull/29/hovercard\" href=\"https://github.com/EBI-Metagenomics/HoloFoodR/pull/29\">#29</a>)"}},{"before":"5dcd1cf4190e342e99a8f190afdbfa122f38be93","after":"b28072c8336ecbc7e373e72323ea85eb60997257","ref":"refs/heads/gh-pages","pushedAt":"2024-06-27T17:47:22.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"github-actions[bot]","name":null,"path":"/apps/github-actions","primaryAvatarUrl":"https://avatars.githubusercontent.com/in/15368?s=80&v=4"},"commit":{"message":"Deploying to gh-pages from @ EBI-Metagenomics/HoloFoodR@277977cb7a9b68edfcc59ab81710123aecaaf13c 🚀","shortMessageHtmlLink":"Deploying to gh-pages from @ <a class=\"commit-link\" data-hovercard-type=\"commit\" data-hovercard-url=\"https://github.com/EBI-Metagenomics/HoloFoodR/commit/277977cb7a9b68edfcc59ab81710123aecaaf13c/hovercard\" href=\"https://github.com/EBI-Metagenomics/HoloFoodR/commit/277977cb7a9b68edfcc59ab81710123aecaaf13c\"><tt>277977c</tt></a> 🚀"}},{"before":"49e8e1248f9b1a284199eb9bcdf298bd1a57b145","after":"5dcd1cf4190e342e99a8f190afdbfa122f38be93","ref":"refs/heads/gh-pages","pushedAt":"2024-06-27T17:42:21.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"github-actions[bot]","name":null,"path":"/apps/github-actions","primaryAvatarUrl":"https://avatars.githubusercontent.com/in/15368?s=80&v=4"},"commit":{"message":"Deploying to gh-pages from @ EBI-Metagenomics/HoloFoodR@b92c92a0c9e932d5ee96f7475b555ed938718e71 🚀","shortMessageHtmlLink":"Deploying to gh-pages from @ <a class=\"commit-link\" data-hovercard-type=\"commit\" data-hovercard-url=\"https://github.com/EBI-Metagenomics/HoloFoodR/commit/b92c92a0c9e932d5ee96f7475b555ed938718e71/hovercard\" href=\"https://github.com/EBI-Metagenomics/HoloFoodR/commit/b92c92a0c9e932d5ee96f7475b555ed938718e71\"><tt>b92c92a</tt></a> 🚀"}},{"before":"4e945ffa566dcdfbdf19fd50bd8b5e190bce98cd","after":"fc5c0e5c1ff93c2a04585769ab73e64268bcc4be","ref":"refs/heads/fixes","pushedAt":"2024-06-27T17:35:31.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"TuomasBorman","name":"Tuomas Borman","path":"/TuomasBorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/60338854?s=80&v=4"},"commit":{"message":"up","shortMessageHtmlLink":"up"}},{"before":"737983440ce72b6b7af5d16c52c92f991c078a38","after":"4e945ffa566dcdfbdf19fd50bd8b5e190bce98cd","ref":"refs/heads/fixes","pushedAt":"2024-06-27T17:29:02.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"TuomasBorman","name":"Tuomas Borman","path":"/TuomasBorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/60338854?s=80&v=4"},"commit":{"message":"up","shortMessageHtmlLink":"up"}},{"before":null,"after":"737983440ce72b6b7af5d16c52c92f991c078a38","ref":"refs/heads/fixes","pushedAt":"2024-06-27T17:26:28.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"TuomasBorman","name":"Tuomas Borman","path":"/TuomasBorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/60338854?s=80&v=4"},"commit":{"message":"Fixes for Bioconductor submission (#28)","shortMessageHtmlLink":"Fixes for Bioconductor submission (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2337953066\" data-permission-text=\"Title is private\" data-url=\"https://github.com/EBI-Metagenomics/HoloFoodR/issues/28\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/EBI-Metagenomics/HoloFoodR/pull/28/hovercard\" href=\"https://github.com/EBI-Metagenomics/HoloFoodR/pull/28\">#28</a>)"}},{"before":"002ab3d29539cd547f2fa9851af0bea19a725c07","after":"3111e6be96332f7dbe655e24e5c0c1f7e0dd40a0","ref":"refs/heads/case-study","pushedAt":"2024-06-27T10:59:04.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"artur-sannikov","name":"Artur Sannikov","path":"/artur-sannikov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/40318410?s=80&v=4"},"commit":{"message":"Add: more explanations to cross-association analysis","shortMessageHtmlLink":"Add: more explanations to cross-association analysis"}},{"before":"a9a7f40547ea18bef6670df3ee85766ff67a30c9","after":"002ab3d29539cd547f2fa9851af0bea19a725c07","ref":"refs/heads/case-study","pushedAt":"2024-06-27T10:30:10.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"artur-sannikov","name":"Artur Sannikov","path":"/artur-sannikov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/40318410?s=80&v=4"},"commit":{"message":"Remove fdr correction from Shannon index, there are not multiple comparisons","shortMessageHtmlLink":"Remove fdr correction from Shannon index, there are not multiple comp…"}},{"before":"cb76990048140d59f513e46419b8d0be524c5e85","after":"a9a7f40547ea18bef6670df3ee85766ff67a30c9","ref":"refs/heads/case-study","pushedAt":"2024-06-27T10:27:57.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"artur-sannikov","name":"Artur Sannikov","path":"/artur-sannikov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/40318410?s=80&v=4"},"commit":{"message":"Update references","shortMessageHtmlLink":"Update references"}},{"before":"384e7c8a79982747354f4c1b916ef14ee0e67d65","after":"cb76990048140d59f513e46419b8d0be524c5e85","ref":"refs/heads/case-study","pushedAt":"2024-06-27T10:10:41.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"artur-sannikov","name":"Artur Sannikov","path":"/artur-sannikov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/40318410?s=80&v=4"},"commit":{"message":"Update files","shortMessageHtmlLink":"Update files"}},{"before":"e5a7498c43ddfa29ca5831baca51f49fe5320ccc","after":"384e7c8a79982747354f4c1b916ef14ee0e67d65","ref":"refs/heads/case-study","pushedAt":"2024-06-27T07:54:05.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"artur-sannikov","name":"Artur Sannikov","path":"/artur-sannikov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/40318410?s=80&v=4"},"commit":{"message":"Add: explanations on data pre-processing","shortMessageHtmlLink":"Add: explanations on data pre-processing"}},{"before":"ea5f10ad4820bc145ec60bda32c583c0aeaf917e","after":"e5a7498c43ddfa29ca5831baca51f49fe5320ccc","ref":"refs/heads/case-study","pushedAt":"2024-06-27T07:01:47.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"artur-sannikov","name":"Artur Sannikov","path":"/artur-sannikov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/40318410?s=80&v=4"},"commit":{"message":"Add: explanations to 'Retrieve HoloFood data' step","shortMessageHtmlLink":"Add: explanations to 'Retrieve HoloFood data' step"}},{"before":"c2de89277b55021c30c0a7a59f86d97f1cb4cfc5","after":"e114874b112eea1d6e78d675802e8b78b2cf0c12","ref":"refs/heads/cleanup","pushedAt":"2024-06-26T13:46:21.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"artur-sannikov","name":"Artur Sannikov","path":"/artur-sannikov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/40318410?s=80&v=4"},"commit":{"message":"Do not plot variance explained","shortMessageHtmlLink":"Do not plot variance explained"}},{"before":"70e08de77a636032a4ce9ef3ff06d0b2dd5873a0","after":"ea5f10ad4820bc145ec60bda32c583c0aeaf917e","ref":"refs/heads/case-study","pushedAt":"2024-06-26T12:30:32.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"artur-sannikov","name":"Artur Sannikov","path":"/artur-sannikov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/40318410?s=80&v=4"},"commit":{"message":"Update html","shortMessageHtmlLink":"Update html"}},{"before":"14650a75f45b3ec29df857716f06da4e30413488","after":"70e08de77a636032a4ce9ef3ff06d0b2dd5873a0","ref":"refs/heads/case-study","pushedAt":"2024-06-26T08:45:55.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"artur-sannikov","name":"Artur Sannikov","path":"/artur-sannikov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/40318410?s=80&v=4"},"commit":{"message":"Add: html figures","shortMessageHtmlLink":"Add: html figures"}},{"before":"eed8d3e6b625ebb4deaf7e6125a4d18a539fda58","after":"14650a75f45b3ec29df857716f06da4e30413488","ref":"refs/heads/case-study","pushedAt":"2024-06-25T14:09:05.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"artur-sannikov","name":"Artur Sannikov","path":"/artur-sannikov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/40318410?s=80&v=4"},"commit":{"message":"Update RDS files","shortMessageHtmlLink":"Update RDS files"}},{"before":"a9edccc4bca305807718824a977421045a2d24ad","after":"eed8d3e6b625ebb4deaf7e6125a4d18a539fda58","ref":"refs/heads/case-study","pushedAt":"2024-06-25T14:08:35.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"artur-sannikov","name":"Artur Sannikov","path":"/artur-sannikov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/40318410?s=80&v=4"},"commit":{"message":"Change: most recent Containerfile","shortMessageHtmlLink":"Change: most recent Containerfile"}},{"before":"08a65020a908a5e51a1c1693850f9ff87fb73c3b","after":"a9edccc4bca305807718824a977421045a2d24ad","ref":"refs/heads/case-study","pushedAt":"2024-06-25T13:58:43.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"artur-sannikov","name":"Artur Sannikov","path":"/artur-sannikov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/40318410?s=80&v=4"},"commit":{"message":"Remove UpSetR package","shortMessageHtmlLink":"Remove UpSetR package"}},{"before":"3ed18a0b9a6e758fae2f20255771fee2dd4de06b","after":"08a65020a908a5e51a1c1693850f9ff87fb73c3b","ref":"refs/heads/case-study","pushedAt":"2024-06-25T13:42:37.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"artur-sannikov","name":"Artur Sannikov","path":"/artur-sannikov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/40318410?s=80&v=4"},"commit":{"message":"Add: stricter variation filtering for cross-association analysis","shortMessageHtmlLink":"Add: stricter variation filtering for cross-association analysis"}},{"before":"9000af6654208b94cd88cef77d556f9d378b73d3","after":"3ed18a0b9a6e758fae2f20255771fee2dd4de06b","ref":"refs/heads/case-study","pushedAt":"2024-06-25T13:28:12.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"artur-sannikov","name":"Artur Sannikov","path":"/artur-sannikov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/40318410?s=80&v=4"},"commit":{"message":"Add: alpha-diversity","shortMessageHtmlLink":"Add: alpha-diversity"}},{"before":"dd9e5ed46f1bf26ea39c01d2f68a5bd172822166","after":"9000af6654208b94cd88cef77d556f9d378b73d3","ref":"refs/heads/case-study","pushedAt":"2024-06-25T12:06:10.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"artur-sannikov","name":"Artur Sannikov","path":"/artur-sannikov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/40318410?s=80&v=4"},"commit":{"message":"Add: bartMachine-based classification","shortMessageHtmlLink":"Add: bartMachine-based classification"}},{"before":"813d777e159310940709d5fdac502bbf5cc39b89","after":"dd9e5ed46f1bf26ea39c01d2f68a5bd172822166","ref":"refs/heads/case-study","pushedAt":"2024-06-25T12:05:02.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"artur-sannikov","name":"Artur Sannikov","path":"/artur-sannikov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/40318410?s=80&v=4"},"commit":{"message":"Add: bartMachine-based classification","shortMessageHtmlLink":"Add: bartMachine-based classification"}},{"before":"946f62b976102edb8cd16db8d5bc0f28e7f68fb7","after":"813d777e159310940709d5fdac502bbf5cc39b89","ref":"refs/heads/case-study","pushedAt":"2024-06-25T10:43:43.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"artur-sannikov","name":"Artur Sannikov","path":"/artur-sannikov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/40318410?s=80&v=4"},"commit":{"message":"Fix html generation; add more explanation to random forest","shortMessageHtmlLink":"Fix html generation; add more explanation to random forest"}},{"before":"2b9828d38e10ac4b41cb6fbc558d449f10747165","after":"946f62b976102edb8cd16db8d5bc0f28e7f68fb7","ref":"refs/heads/case-study","pushedAt":"2024-06-25T07:24:07.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"artur-sannikov","name":"Artur Sannikov","path":"/artur-sannikov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/40318410?s=80&v=4"},"commit":{"message":"Add: html output","shortMessageHtmlLink":"Add: html output"}},{"before":"3c67ca61de0436aebf5a441a7e6963507dd28c9c","after":"2b9828d38e10ac4b41cb6fbc558d449f10747165","ref":"refs/heads/case-study","pushedAt":"2024-06-25T07:21:55.000Z","pushType":"push","commitsCount":5,"pusher":{"login":"artur-sannikov","name":"Artur Sannikov","path":"/artur-sannikov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/40318410?s=80&v=4"},"commit":{"message":"Add: do not include chunk outputs","shortMessageHtmlLink":"Add: do not include chunk outputs"}},{"before":"661a104bf5fabb18ec51bd42789a049b129e5efb","after":"3c67ca61de0436aebf5a441a7e6963507dd28c9c","ref":"refs/heads/case-study","pushedAt":"2024-06-24T07:06:20.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"artur-sannikov","name":"Artur Sannikov","path":"/artur-sannikov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/40318410?s=80&v=4"},"commit":{"message":"Remove manully computed prevalence","shortMessageHtmlLink":"Remove manully computed prevalence"}},{"before":"d1d3f2d3e563a1add429cf24f512e79b4a3709e9","after":"661a104bf5fabb18ec51bd42789a049b129e5efb","ref":"refs/heads/case-study","pushedAt":"2024-06-24T06:17:53.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"artur-sannikov","name":"Artur Sannikov","path":"/artur-sannikov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/40318410?s=80&v=4"},"commit":{"message":"Change all T to TRUE","shortMessageHtmlLink":"Change all T to TRUE"}},{"before":"00f66d1cefea9fbefadb9d91373f1348c9e9db00","after":"d1d3f2d3e563a1add429cf24f512e79b4a3709e9","ref":"refs/heads/case-study","pushedAt":"2024-06-20T13:10:11.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"artur-sannikov","name":"Artur Sannikov","path":"/artur-sannikov","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/40318410?s=80&v=4"},"commit":{"message":"Add: more explanations to IntegratedLearner section","shortMessageHtmlLink":"Add: more explanations to IntegratedLearner section"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEcSDFxAA","startCursor":null,"endCursor":null}},"title":"Activity · EBI-Metagenomics/HoloFoodR"}