{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":237112652,"defaultBranch":"master","name":"mutperiod","ownerLogin":"bmorledge-hampton19","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2020-01-30T00:50:48.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/22180776?v=4","public":true,"private":false,"isOrgOwned":false},"refInfo":{"name":"","listCacheKey":"v0:1580345456.0","currentOid":""},"activityList":{"items":[{"before":"b4e355c0eb82f281a7075f9fbc28d55e9add7272","after":"a430e039159ea4b36c59981ef857e145ce114499","ref":"refs/heads/master","pushedAt":"2024-03-06T04:37:14.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bmorledge-hampton19","name":"Benjamin Morledge-Hampton","path":"/bmorledge-hampton19","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/22180776?s=80&v=4"},"commit":{"message":"Clarified the dialog which creates the data dir\n\nThe dialog now makes it clear that the data directory is being created for mutperiod.","shortMessageHtmlLink":"Clarified the dialog which creates the data dir"}},{"before":"aa0aff0154dbefd98c56b4ee08fae21aa4db4083","after":"b4e355c0eb82f281a7075f9fbc28d55e9add7272","ref":"refs/heads/master","pushedAt":"2024-03-05T19:36:48.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"bmorledge-hampton19","name":"Benjamin Morledge-Hampton","path":"/bmorledge-hampton19","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/22180776?s=80&v=4"},"commit":{"message":"Added rotational positioning transition states\n\n- Added ranges for rotational transition states (minor-in to minor-out and minor-out to minor-in) derived from minor-in and minor-out positions.\n- Added options to color periodicity plots by these transition states, which also included adding them to the nucleosome color palette.\n- Finally decided to designate the area surrounding the dyad axis as \"minor-out\". I mean, come on. Even if it looks a little different, what other direction is the minor groove going to be facing there?","shortMessageHtmlLink":"Added rotational positioning transition states"}},{"before":"5dcb88e20e4f3866276927ca39f8c51b491e191c","after":"aa0aff0154dbefd98c56b4ee08fae21aa4db4083","ref":"refs/heads/master","pushedAt":"2024-02-20T06:10:36.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bmorledge-hampton19","name":"Benjamin Morledge-Hampton","path":"/bmorledge-hampton19","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/22180776?s=80&v=4"},"commit":{"message":"Added option to overlay smoothed counts on raw\n\n- When smoothing translational data, a new column is created instead of overwriting the original column.\n- Updated NucleosomeColorPalette to include colors for underlaid raw counts.\n- Added option to overlay smoothed counts on raw counts for both the plotPeriodicity and plotAndParsePeriodicity functions.","shortMessageHtmlLink":"Added option to overlay smoothed counts on raw"}},{"before":"ab1b3b81c34b73ff6f7d47f6da1e7878616564d2","after":"5dcb88e20e4f3866276927ca39f8c51b491e191c","ref":"refs/heads/master","pushedAt":"2024-02-05T23:25:57.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"bmorledge-hampton19","name":"Benjamin Morledge-Hampton","path":"/bmorledge-hampton19","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/22180776?s=80&v=4"},"commit":{"message":"Added options for stranded analysis\n\nBy default, mutperiod arbitrarily assigns all nucleosomes to the plus strand. However, this is not desirable when repurposing this pipeline for stranded features, such as transcription factor binding sites. The changes were made in three key areas:\n- Counting features about \"nucleosomes\"\n- Generating background counts relative to sequence context.\n- Using another data set as background.","shortMessageHtmlLink":"Added options for stranded analysis"}},{"before":"91b16a567a1140fe88cf56a65f1a439f13eb5d29","after":"ab1b3b81c34b73ff6f7d47f6da1e7878616564d2","ref":"refs/heads/master","pushedAt":"2024-01-13T00:15:19.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bmorledge-hampton19","name":"Benjamin Morledge-Hampton","path":"/bmorledge-hampton19","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/22180776?s=80&v=4"},"commit":{"message":"Bugfix related to modifying reference vs. copy","shortMessageHtmlLink":"Bugfix related to modifying reference vs. copy"}},{"before":"a1405a1497c0903f0d9bfa959ccf760b611e449a","after":"91b16a567a1140fe88cf56a65f1a439f13eb5d29","ref":"refs/heads/master","pushedAt":"2023-12-20T00:38:09.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bmorledge-hampton19","name":"Benjamin Morledge-Hampton","path":"/bmorledge-hampton19","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/22180776?s=80&v=4"},"commit":{"message":"Fixed bug where legend titles were not removed","shortMessageHtmlLink":"Fixed bug where legend titles were not removed"}},{"before":"32c2487602c87cae15441d874ba85a434828ba93","after":"a1405a1497c0903f0d9bfa959ccf760b611e449a","ref":"refs/heads/master","pushedAt":"2023-12-18T20:26:06.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bmorledge-hampton19","name":"Benjamin Morledge-Hampton","path":"/bmorledge-hampton19","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/22180776?s=80&v=4"},"commit":{"message":"ParseXRSeq now returns parsed file paths","shortMessageHtmlLink":"ParseXRSeq now returns parsed file paths"}},{"before":"6bf96244f9ba03b6dbbec26e5b0d4d26a898704e","after":"32c2487602c87cae15441d874ba85a434828ba93","ref":"refs/heads/master","pushedAt":"2023-12-18T20:06:58.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bmorledge-hampton19","name":"Benjamin Morledge-Hampton","path":"/bmorledge-hampton19","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/22180776?s=80&v=4"},"commit":{"message":"Added PresetCallParams Enum.\n\nThis Enum serves as a way for external scripts to use the call params files that are internal to the mutperiod pipeline.","shortMessageHtmlLink":"Added PresetCallParams Enum."}},{"before":"c4ac7aeff109fdc1e90ea37d213263baf188f149","after":"6bf96244f9ba03b6dbbec26e5b0d4d26a898704e","ref":"refs/heads/master","pushedAt":"2023-12-11T21:38:21.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bmorledge-hampton19","name":"Benjamin Morledge-Hampton","path":"/bmorledge-hampton19","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/22180776?s=80&v=4"},"commit":{"message":"Create GeneratePlotnineFigures.py\n\nPorted over periodicity plotting from R to Python. This was a bit of a chore with more changes than are worth listing here, but everything seems to be working for the time being!","shortMessageHtmlLink":"Create GeneratePlotnineFigures.py"}},{"before":"513aa90115f00a588272f608b3dbac63ec6c0682","after":"c4ac7aeff109fdc1e90ea37d213263baf188f149","ref":"refs/heads/master","pushedAt":"2023-12-11T21:31:47.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bmorledge-hampton19","name":"Benjamin Morledge-Hampton","path":"/bmorledge-hampton19","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/22180776?s=80&v=4"},"commit":{"message":"Modernized ParseAlexandrov\n\n- Nucleosome map is no longer passed with initial Metadata.\n- parseCustomBed is explicitly told to only use single base substitutions.\n- Added \"alexandrov\" to the InputFormat enum.","shortMessageHtmlLink":"Modernized ParseAlexandrov"}},{"before":"0b9fc58406a7c22915b7852a067e820a299100ba","after":"513aa90115f00a588272f608b3dbac63ec6c0682","ref":"refs/heads/master","pushedAt":"2023-11-27T20:46:38.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bmorledge-hampton19","name":"Benjamin Morledge-Hampton","path":"/bmorledge-hampton19","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/22180776?s=80&v=4"},"commit":{"message":"Added getNRL parameter to regenerate file\n\nPreviously, files were always regenerated.","shortMessageHtmlLink":"Added getNRL parameter to regenerate file"}},{"before":"ce9afc2929e3ea5f6de7bbe2757495f24c9fe500","after":"0b9fc58406a7c22915b7852a067e820a299100ba","ref":"refs/heads/master","pushedAt":"2023-06-30T19:13:40.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bmorledge-hampton19","name":"Benjamin Morledge-Hampton","path":"/bmorledge-hampton19","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/22180776?s=80&v=4"},"commit":{"message":"Add dialog titles","shortMessageHtmlLink":"Add dialog titles"}}],"hasNextPage":false,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEDYlUyQA","startCursor":null,"endCursor":null}},"title":"Activity · bmorledge-hampton19/mutperiod"}