{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":263015723,"defaultBranch":"master","name":"SQANTI3","ownerLogin":"ConesaLab","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2020-05-11T10:52:56.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/29752440?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1717071029.0","currentOid":""},"activityList":{"items":[{"before":"9f0e6b702bacfec1d73dbf3d3a33509e9e6898c1","after":null,"ref":"refs/heads/genic_nic","pushedAt":"2024-05-30T12:10:29.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"alexpan00","name":"Alejandro Panaigua","path":"/alexpan00","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/84267364?s=80&v=4"}},{"before":"f77e8786a43f4855a16b25b72f45e9d67315a767","after":"a7c26807e5d24e0f131ff627ad5985635ce29cb8","ref":"refs/heads/master","pushedAt":"2024-05-30T12:10:05.000Z","pushType":"pr_merge","commitsCount":4,"pusher":{"login":"alexpan00","name":"Alejandro Panaigua","path":"/alexpan00","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/84267364?s=80&v=4"},"commit":{"message":"Merge pull request #303 from ConesaLab/genic_nic\n\nCorrection of the classfication of mono-exons","shortMessageHtmlLink":"Merge pull request #303 from ConesaLab/genic_nic"}},{"before":"9022a32a7c1b00575b4b19bc4656a212de89d3eb","after":"9f0e6b702bacfec1d73dbf3d3a33509e9e6898c1","ref":"refs/heads/genic_nic","pushedAt":"2024-05-30T11:42:57.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"alexpan00","name":"Alejandro Panaigua","path":"/alexpan00","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/84267364?s=80&v=4"},"commit":{"message":"Fixed a bug in the classification of mono-exon ISM + update documentation","shortMessageHtmlLink":"Fixed a bug in the classification of mono-exon ISM + update documenta…"}},{"before":"3275a7f354d31e2d8b3e7bd5ed9d32abfaabe571","after":"9022a32a7c1b00575b4b19bc4656a212de89d3eb","ref":"refs/heads/genic_nic","pushedAt":"2024-05-30T10:28:35.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"alexpan00","name":"Alejandro Panaigua","path":"/alexpan00","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/84267364?s=80&v=4"},"commit":{"message":"Classify as genic in the proper function","shortMessageHtmlLink":"Classify as genic in the proper function"}},{"before":"f77e8786a43f4855a16b25b72f45e9d67315a767","after":"3275a7f354d31e2d8b3e7bd5ed9d32abfaabe571","ref":"refs/heads/genic_nic","pushedAt":"2024-05-30T09:07:22.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"alexpan00","name":"Alejandro Panaigua","path":"/alexpan00","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/84267364?s=80&v=4"},"commit":{"message":"Monoexons that don't overlap a entire junction will be considered genic, not NIC. Only when the monoexon spans a whole intron will be considered NIC by intron retention","shortMessageHtmlLink":"Monoexons that don't overlap a entire junction will be considered gen…"}},{"before":null,"after":"f77e8786a43f4855a16b25b72f45e9d67315a767","ref":"refs/heads/genic_nic","pushedAt":"2024-05-30T09:04:30.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"alexpan00","name":"Alejandro Panaigua","path":"/alexpan00","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/84267364?s=80&v=4"},"commit":{"message":"Update sqanti3_qc.py\n\nRun STAR mapping outside of main SQANTI3 run.","shortMessageHtmlLink":"Update sqanti3_qc.py"}},{"before":"b6cade844fdb015a7162fdbbdad7b91746330ed2","after":"095a08e5e3b172d56b129c072da9c67337d21d31","ref":"refs/heads/sqanti-reads","pushedAt":"2024-05-20T16:30:15.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"netanyak","name":null,"path":"/netanyak","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/113125696?s=80&v=4"},"commit":{"message":"Add updated plotting script","shortMessageHtmlLink":"Add updated plotting script"}},{"before":"403648693ac295fe3955e78d657bde8ebf82f956","after":"f77e8786a43f4855a16b25b72f45e9d67315a767","ref":"refs/heads/master","pushedAt":"2024-05-15T02:05:16.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lkondratova","name":"Liudmyla Kondratova","path":"/lkondratova","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/47575662?s=80&v=4"},"commit":{"message":"Update sqanti3_qc.py\n\nRun STAR mapping outside of main SQANTI3 run.","shortMessageHtmlLink":"Update sqanti3_qc.py"}},{"before":"909f09690220100de6e1dc6af313224d09f1f945","after":"403648693ac295fe3955e78d657bde8ebf82f956","ref":"refs/heads/master","pushedAt":"2024-05-13T21:49:37.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lkondratova","name":"Liudmyla Kondratova","path":"/lkondratova","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/47575662?s=80&v=4"},"commit":{"message":"Update short_reads.py\n\nFixed typo, line 197","shortMessageHtmlLink":"Update short_reads.py"}},{"before":"6345adf8694a96ec1ee0bf9b3ba7ea89f11d2cb9","after":"909f09690220100de6e1dc6af313224d09f1f945","ref":"refs/heads/master","pushedAt":"2024-05-13T08:30:58.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"carolinamonzo","name":"Carolina Monzó","path":"/carolinamonzo","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24670602?s=80&v=4"},"commit":{"message":"Update release link","shortMessageHtmlLink":"Update release link"}},{"before":"29974c1c01dddc5ac403ba73de5b14b0dcc2c0b8","after":"6345adf8694a96ec1ee0bf9b3ba7ea89f11d2cb9","ref":"refs/heads/master","pushedAt":"2024-05-09T09:37:59.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"alexpan00","name":"Alejandro Panaigua","path":"/alexpan00","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/84267364?s=80&v=4"},"commit":{"message":"Update err_correct_w_genome.py\n\nFixed and error importing the class BioReaders","shortMessageHtmlLink":"Update err_correct_w_genome.py"}},{"before":"bc589a3690802089c3cc472cd645f6a471a18ae9","after":"b6cade844fdb015a7162fdbbdad7b91746330ed2","ref":"refs/heads/sqanti-reads","pushedAt":"2024-05-08T19:48:42.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"netanyak","name":null,"path":"/netanyak","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/113125696?s=80&v=4"},"commit":{"message":"Add files via upload","shortMessageHtmlLink":"Add files via upload"}},{"before":"53149c4f65c85b414cab04b3a0e4a0a03fcb64a7","after":"29974c1c01dddc5ac403ba73de5b14b0dcc2c0b8","ref":"refs/heads/master","pushedAt":"2024-05-06T16:15:31.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"TianYuan-Liu","name":"Tianyuan Liu","path":"/TianYuan-Liu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/59029869?s=80&v=4"},"commit":{"message":"Fix Intra-Priming Quality by structure category: Replace has_data with render_ggplotly()\n\nThis commit addresses an issue with the Intra-Priming Quality Check (by structure category) where the has_data function was not working properly. The function is now changed to render_ggplotly() to ensure correct functionality.","shortMessageHtmlLink":"Fix Intra-Priming Quality by structure category: Replace has_data wit…"}},{"before":"63d1419d0e893ef15a9c3f8e9f60136e281dda42","after":"53149c4f65c85b414cab04b3a0e4a0a03fcb64a7","ref":"refs/heads/master","pushedAt":"2024-05-06T14:35:44.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"TianYuan-Liu","name":"Tianyuan Liu","path":"/TianYuan-Liu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/59029869?s=80&v=4"},"commit":{"message":"Removed debug args","shortMessageHtmlLink":"Removed debug args"}},{"before":"4fb4a752bf034d2907d8c33686782a80876727a9","after":"63d1419d0e893ef15a9c3f8e9f60136e281dda42","ref":"refs/heads/master","pushedAt":"2024-05-06T14:34:13.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"TianYuan-Liu","name":"Tianyuan Liu","path":"/TianYuan-Liu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/59029869?s=80&v=4"},"commit":{"message":"Improve error handling in Rmd script for robust plot rendering\n\n- Add `render_ggplotly` function to check for non-empty plot data before rendering.\n- Replace direct `ggplotly()` calls with safer `render_ggplotly()` to prevent crashes on empty data.\n- Implement user feedback for missing or incomplete plot data for easier debugging.","shortMessageHtmlLink":"Improve error handling in Rmd script for robust plot rendering"}},{"before":"d9b7390a4aae980def3924348bcd1eadd8d7bd73","after":"bc589a3690802089c3cc472cd645f6a471a18ae9","ref":"refs/heads/sqanti-reads","pushedAt":"2024-04-28T19:04:32.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"carolinamonzo","name":"Carolina Monzó","path":"/carolinamonzo","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24670602?s=80&v=4"},"commit":{"message":"adding junction hash","shortMessageHtmlLink":"adding junction hash"}},{"before":"5af4f2b7cb41b3be2be98c7bf9857c2e6806e130","after":"4fb4a752bf034d2907d8c33686782a80876727a9","ref":"refs/heads/master","pushedAt":"2024-04-24T10:45:45.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"TianYuan-Liu","name":"Tianyuan Liu","path":"/TianYuan-Liu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/59029869?s=80&v=4"},"commit":{"message":"Add badges to README\n\nIncorporated status badges from Shields.io to the README to provide real-time status updates on the repository. This badge helps visitors quickly gauge the current health and stability of the project.","shortMessageHtmlLink":"Add badges to README"}},{"before":"56e7bbe42aa22b0778980e423394adf9edcebc4d","after":"d9b7390a4aae980def3924348bcd1eadd8d7bd73","ref":"refs/heads/sqanti-reads","pushedAt":"2024-04-18T16:42:58.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"carolinamonzo","name":"Carolina Monzó","path":"/carolinamonzo","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24670602?s=80&v=4"},"commit":{"message":"fixing typo in junctions","shortMessageHtmlLink":"fixing typo in junctions"}},{"before":"a299ad1e870834ee1c6d0f81d7eaead786ec8718","after":"56e7bbe42aa22b0778980e423394adf9edcebc4d","ref":"refs/heads/sqanti-reads","pushedAt":"2024-04-18T15:15:24.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"carolinamonzo","name":"Carolina Monzó","path":"/carolinamonzo","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24670602?s=80&v=4"},"commit":{"message":"adding structure for sqantireads","shortMessageHtmlLink":"adding structure for sqantireads"}},{"before":"8ebd7f4b01fbd094fa114f8ec988ba8432d52f61","after":"a299ad1e870834ee1c6d0f81d7eaead786ec8718","ref":"refs/heads/sqanti-reads","pushedAt":"2024-04-15T15:57:11.000Z","pushType":"push","commitsCount":34,"pusher":{"login":"carolinamonzo","name":"Carolina Monzó","path":"/carolinamonzo","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24670602?s=80&v=4"},"commit":{"message":"Merge remote-tracking branch 'origin/master' into sqanti-reads","shortMessageHtmlLink":"Merge remote-tracking branch 'origin/master' into sqanti-reads"}},{"before":"ab3fc7d5408d245089639021bcc04c5709224cdc","after":"5af4f2b7cb41b3be2be98c7bf9857c2e6806e130","ref":"refs/heads/master","pushedAt":"2024-04-11T13:53:46.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"TianYuan-Liu","name":"Tianyuan Liu","path":"/TianYuan-Liu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/59029869?s=80&v=4"},"commit":{"message":"Resolved Parallelization Error (Issue #243) caused by improperly formatted GTF files. To address this issue, we've updated our approach by setting clear expectations for the formatting of GTF files when parsed using collapseGFFReader. Additionally, for writing files associated with each chunk of data, we've transitioned to using pandas. This choice was made because pandas provides greater flexibility and efficiency, especially when dealing with formatting edge cases. These updates ensure that the parallelization process remains seamless and error-free, even when handling non-standard GTF files.","shortMessageHtmlLink":"Resolved Parallelization Error (Issue #243) caused by improperly form…"}},{"before":"08da9b81ecd60d92073d6bf9f95e0088c32829ff","after":"ab3fc7d5408d245089639021bcc04c5709224cdc","ref":"refs/heads/master","pushedAt":"2024-04-10T14:03:22.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"alexpan00","name":"Alejandro Panaigua","path":"/alexpan00","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/84267364?s=80&v=4"},"commit":{"message":"Fixed a bug where SQANTI3 failed when there were transcripts in the input further to 3' than the most 3' transcript of the reference.","shortMessageHtmlLink":"Fixed a bug where SQANTI3 failed when there were transcripts in the i…"}},{"before":"e7054ab732ce71756c2f402df70d448d052e5c17","after":"08da9b81ecd60d92073d6bf9f95e0088c32829ff","ref":"refs/heads/master","pushedAt":"2024-04-02T23:42:51.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lkondratova","name":"Liudmyla Kondratova","path":"/lkondratova","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/47575662?s=80&v=4"},"commit":{"message":"Minor improvements.","shortMessageHtmlLink":"Minor improvements."}},{"before":"18fdcd2d3e13e4a29cc7d1e9df5f03baf58f4fad","after":null,"ref":"refs/heads/genic_intron","pushedAt":"2024-04-02T15:15:18.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"carolinamonzo","name":"Carolina Monzó","path":"/carolinamonzo","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24670602?s=80&v=4"}},{"before":"2dbc5841827d2f4d46d3d93636bc44a1f54b3532","after":null,"ref":"refs/heads/min_ref_len","pushedAt":"2024-04-02T15:13:50.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"carolinamonzo","name":"Carolina Monzó","path":"/carolinamonzo","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24670602?s=80&v=4"}},{"before":"c9cb1607b7ec119ded7d824808657debab34c3cb","after":"e7054ab732ce71756c2f402df70d448d052e5c17","ref":"refs/heads/master","pushedAt":"2024-04-02T15:09:49.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"alexpan00","name":"Alejandro Panaigua","path":"/alexpan00","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/84267364?s=80&v=4"},"commit":{"message":"Merge pull request #283 from ConesaLab/genic_intron\n\nFixed a bug on classification of genic_intron (issue #255)","shortMessageHtmlLink":"Merge pull request #283 from ConesaLab/genic_intron"}},{"before":null,"after":"18fdcd2d3e13e4a29cc7d1e9df5f03baf58f4fad","ref":"refs/heads/genic_intron","pushedAt":"2024-04-02T15:05:03.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"alexpan00","name":"Alejandro Panaigua","path":"/alexpan00","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/84267364?s=80&v=4"},"commit":{"message":"Fixed a bug on classification of genic_intron (issue #255)","shortMessageHtmlLink":"Fixed a bug on classification of genic_intron (issue #255)"}},{"before":"401c0c25ffeb96d3ad9578a99ace307cd4409d58","after":null,"ref":"refs/heads/issue_template","pushedAt":"2024-03-29T19:02:27.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"carolinamonzo","name":"Carolina Monzó","path":"/carolinamonzo","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24670602?s=80&v=4"}},{"before":"79893c7a0176ae7cb09cb4bab2753ec117ddba38","after":"c9cb1607b7ec119ded7d824808657debab34c3cb","ref":"refs/heads/master","pushedAt":"2024-03-29T18:45:36.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"lkondratova","name":"Liudmyla Kondratova","path":"/lkondratova","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/47575662?s=80&v=4"},"commit":{"message":"Merge pull request #280 from ConesaLab/min_ref_len\n\nRecover isoforms shorter than min_ref_len.","shortMessageHtmlLink":"Merge pull request #280 from ConesaLab/min_ref_len"}},{"before":"894009780459f8b51350edecd6c4c77104f1e8b7","after":"79893c7a0176ae7cb09cb4bab2753ec117ddba38","ref":"refs/heads/master","pushedAt":"2024-03-27T15:46:08.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"TianYuan-Liu","name":"Tianyuan Liu","path":"/TianYuan-Liu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/59029869?s=80&v=4"},"commit":{"message":"fix html report howtouse.png","shortMessageHtmlLink":"fix html report howtouse.png"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEV_ieQAA","startCursor":null,"endCursor":null}},"title":"Activity · ConesaLab/SQANTI3"}