{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":626032442,"defaultBranch":"master","name":"spammR","ownerLogin":"PNNL-CompBio","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2023-04-10T16:48:18.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/38365343?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1693342873.0","currentOid":""},"activityList":{"items":[{"before":"950ae0cf61795f6a7ae6767b3a6de1ea9f184ab3","after":"27aada5ec236e313256ac32f357826ec0ac40ceb","ref":"refs/heads/master","pushedAt":"2024-04-04T22:54:13.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"HarkiratSohi","name":null,"path":"/HarkiratSohi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/116124471?s=80&v=4"},"commit":{"message":"Update spatialDiffEx.R\n\nFixed a typo in definition of samp1","shortMessageHtmlLink":"Update spatialDiffEx.R"}},{"before":"e8e2e5b2ff332b24c9107c1eeaa30bba5badbb9a","after":"950ae0cf61795f6a7ae6767b3a6de1ea9f184ab3","ref":"refs/heads/master","pushedAt":"2024-04-04T22:50:09.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"HarkiratSohi","name":null,"path":"/HarkiratSohi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/116124471?s=80&v=4"},"commit":{"message":"Update spatialDiffEx.R","shortMessageHtmlLink":"Update spatialDiffEx.R"}},{"before":"275504f6267b7ea9892abd9ab044655571f45475","after":"e8e2e5b2ff332b24c9107c1eeaa30bba5badbb9a","ref":"refs/heads/master","pushedAt":"2024-04-04T22:49:13.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"HarkiratSohi","name":null,"path":"/HarkiratSohi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/116124471?s=80&v=4"},"commit":{"message":"Update spatialDiffEx.R\n\n- Corrected the order of comparison; code was previously running sample2 vs. sample1. Fixed to run sample1 vs. sample2 \r\n- Updated column names in the output results so they are descriptive of the group comparisons\r\n- Updated what gets returned","shortMessageHtmlLink":"Update spatialDiffEx.R"}},{"before":"7f45e1874633019b3e364db10c67ee96c2b8f7fe","after":"275504f6267b7ea9892abd9ab044655571f45475","ref":"refs/heads/master","pushedAt":"2024-01-24T05:32:35.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"HarkiratSohi","name":null,"path":"/HarkiratSohi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/116124471?s=80&v=4"},"commit":{"message":"Changed package dependency to greater or equal to R 3.5.0","shortMessageHtmlLink":"Changed package dependency to greater or equal to R 3.5.0"}},{"before":"1b824be315f3d6eb2e786596d94a465245905e53","after":"7f45e1874633019b3e364db10c67ee96c2b8f7fe","ref":"refs/heads/master","pushedAt":"2024-01-24T05:28:27.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"HarkiratSohi","name":null,"path":"/HarkiratSohi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/116124471?s=80&v=4"},"commit":{"message":"Re-did \"Imports:\" statements(s) in DESCRIPTION, added BiocManager under Imports:; this should fix the issue of Bioconductor packages that were dependencies not getting automatically installed earlier. Also, added \"BiocViews:\" in the DESCRIPTION file. Fixed import statements in functions.","shortMessageHtmlLink":"Re-did \"Imports:\" statements(s) in DESCRIPTION, added BiocManager und…"}},{"before":"c07efc6a0c8cdc2a236d02ace72304941a02cca1","after":"1b824be315f3d6eb2e786596d94a465245905e53","ref":"refs/heads/master","pushedAt":"2024-01-24T02:16:33.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"HarkiratSohi","name":null,"path":"/HarkiratSohi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/116124471?s=80&v=4"},"commit":{"message":"Update volcanoPlot_DiffExSpe.R\n\nAdded @import statement","shortMessageHtmlLink":"Update volcanoPlot_DiffExSpe.R"}},{"before":"c573a29b6d978135ef7008047e1d2eec9603f6c1","after":"c07efc6a0c8cdc2a236d02ace72304941a02cca1","ref":"refs/heads/master","pushedAt":"2024-01-24T02:15:12.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"HarkiratSohi","name":null,"path":"/HarkiratSohi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/116124471?s=80&v=4"},"commit":{"message":"Update volcanoPlot_DiffExResults.R\n\nAdded @import statement for specific packages needed for the function","shortMessageHtmlLink":"Update volcanoPlot_DiffExResults.R"}},{"before":"969a49dded074a4522e5725a6b57bed75e77fe8f","after":"c573a29b6d978135ef7008047e1d2eec9603f6c1","ref":"refs/heads/master","pushedAt":"2024-01-24T02:14:21.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"HarkiratSohi","name":null,"path":"/HarkiratSohi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/116124471?s=80&v=4"},"commit":{"message":"Update spatialPlot_feature.R\n\nAdded @import statements for specific packages used in the function","shortMessageHtmlLink":"Update spatialPlot_feature.R"}},{"before":"bc118bdc9a6f287f6524b3bb1cbfdb0cd871f6e3","after":"969a49dded074a4522e5725a6b57bed75e77fe8f","ref":"refs/heads/master","pushedAt":"2024-01-24T02:12:02.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"HarkiratSohi","name":null,"path":"/HarkiratSohi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/116124471?s=80&v=4"},"commit":{"message":"Update spatialDiffEx.R\n\nAdded @import limma","shortMessageHtmlLink":"Update spatialDiffEx.R"}},{"before":"b331e355e05c2d433c2f27eeed14b2dac7714089","after":"bc118bdc9a6f287f6524b3bb1cbfdb0cd871f6e3","ref":"refs/heads/master","pushedAt":"2023-09-21T20:03:07.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"HarkiratSohi","name":null,"path":"/HarkiratSohi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/116124471?s=80&v=4"},"commit":{"message":"Make x and y axis have the same scale","shortMessageHtmlLink":"Make x and y axis have the same scale"}},{"before":"2351ec4b211296ffadf8c465ad4fc53e0538b223","after":"b331e355e05c2d433c2f27eeed14b2dac7714089","ref":"refs/heads/master","pushedAt":"2023-09-21T18:55:51.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"HarkiratSohi","name":null,"path":"/HarkiratSohi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/116124471?s=80&v=4"},"commit":{"message":"Fixed function description","shortMessageHtmlLink":"Fixed function description"}},{"before":"b3345a57f8215a857e1d58d63abe8ba1e131f0c1","after":"2351ec4b211296ffadf8c465ad4fc53e0538b223","ref":"refs/heads/master","pushedAt":"2023-09-21T18:43:34.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"HarkiratSohi","name":null,"path":"/HarkiratSohi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/116124471?s=80&v=4"},"commit":{"message":"Testing rexoygen","shortMessageHtmlLink":"Testing rexoygen"}},{"before":"12df71239c66ef6898d5f66346dc9c7a8baf68d2","after":"b3345a57f8215a857e1d58d63abe8ba1e131f0c1","ref":"refs/heads/master","pushedAt":"2023-09-21T17:23:36.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"HarkiratSohi","name":null,"path":"/HarkiratSohi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/116124471?s=80&v=4"},"commit":{"message":"Added parameter for specifiying color for labels on grid squares","shortMessageHtmlLink":"Added parameter for specifiying color for labels on grid squares"}},{"before":"d87980d14ed874732854580423c2f22222a49806","after":"12df71239c66ef6898d5f66346dc9c7a8baf68d2","ref":"refs/heads/master","pushedAt":"2023-09-20T20:21:01.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"HarkiratSohi","name":null,"path":"/HarkiratSohi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/116124471?s=80&v=4"},"commit":{"message":"Update spatialPlot_feature.R\n\nFixed a typo/bug. Changed white to \"white\" for label color","shortMessageHtmlLink":"Update spatialPlot_feature.R"}},{"before":"f611235bc2fb69b170cc977094e0acfa3a47e7ec","after":"d87980d14ed874732854580423c2f22222a49806","ref":"refs/heads/master","pushedAt":"2023-09-20T18:54:30.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"HarkiratSohi","name":null,"path":"/HarkiratSohi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/116124471?s=80&v=4"},"commit":{"message":"Fixed a bug; x and y were not defined. Changed color of sample labels to be white.","shortMessageHtmlLink":"Fixed a bug; x and y were not defined. Changed color of sample labels…"}},{"before":"6727b7ae8ff7d8cf1f3449c8f030076f48e60725","after":"f611235bc2fb69b170cc977094e0acfa3a47e7ec","ref":"refs/heads/master","pushedAt":"2023-08-31T23:20:09.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"HarkiratSohi","name":null,"path":"/HarkiratSohi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/116124471?s=80&v=4"},"commit":{"message":"spatial_coord_type update","shortMessageHtmlLink":"spatial_coord_type update"}},{"before":"5e3b57448e93af04d9ac3d899446d058faa8234e","after":"6727b7ae8ff7d8cf1f3449c8f030076f48e60725","ref":"refs/heads/master","pushedAt":"2023-08-31T23:19:03.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"HarkiratSohi","name":null,"path":"/HarkiratSohi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/116124471?s=80&v=4"},"commit":{"message":"Added spatial_coord_type as an input parameter (in function ())","shortMessageHtmlLink":"Added spatial_coord_type as an input parameter (in function ())"}},{"before":"568d24f3a7a704895e16aadce1542678127a6213","after":"5e3b57448e93af04d9ac3d899446d058faa8234e","ref":"refs/heads/master","pushedAt":"2023-08-31T23:10:11.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"HarkiratSohi","name":null,"path":"/HarkiratSohi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/116124471?s=80&v=4"},"commit":{"message":"Added spatial_coord_type as an input parameter to allow for flexibility in plotting based on the type of position (topleft_corner, topright_corner) of the coordinates for samples.","shortMessageHtmlLink":"Added spatial_coord_type as an input parameter to allow for flexibili…"}},{"before":"97d075bbde0189933623f2bbc2b6155db8603d3e","after":"568d24f3a7a704895e16aadce1542678127a6213","ref":"refs/heads/master","pushedAt":"2023-08-31T00:12:59.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"HarkiratSohi","name":null,"path":"/HarkiratSohi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/116124471?s=80&v=4"},"commit":{"message":"Changed variable \"logTransformed\" to \"log_transformed\"","shortMessageHtmlLink":"Changed variable \"logTransformed\" to \"log_transformed\""}},{"before":"90aaf83f3365c4d952f7bdf6aae20f0df72372e0","after":"97d075bbde0189933623f2bbc2b6155db8603d3e","ref":"refs/heads/master","pushedAt":"2023-08-31T00:09:40.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"HarkiratSohi","name":null,"path":"/HarkiratSohi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/116124471?s=80&v=4"},"commit":{"message":"Changed logTransformed to log_transformed","shortMessageHtmlLink":"Changed logTransformed to log_transformed"}},{"before":"f1df3e614e1cb55490be7ad164f0732dd17953de","after":"90aaf83f3365c4d952f7bdf6aae20f0df72372e0","ref":"refs/heads/master","pushedAt":"2023-08-31T00:07:38.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"HarkiratSohi","name":null,"path":"/HarkiratSohi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/116124471?s=80&v=4"},"commit":{"message":"Modified logTransformed variable","shortMessageHtmlLink":"Modified logTransformed variable"}},{"before":"e70f3e0a12fbc3a1eeb97d8f9d8a4182ca5bde8d","after":"f1df3e614e1cb55490be7ad164f0732dd17953de","ref":"refs/heads/master","pushedAt":"2023-08-30T23:31:57.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"HarkiratSohi","name":null,"path":"/HarkiratSohi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/116124471?s=80&v=4"},"commit":{"message":"Merge branch 'master' of https://github.com/PNNL-CompBio/spammR","shortMessageHtmlLink":"Merge branch 'master' of https://github.com/PNNL-CompBio/spammR"}},{"before":"e910580a9b1dfec16f51fbc12073c513a242bf67","after":"e70f3e0a12fbc3a1eeb97d8f9d8a4182ca5bde8d","ref":"refs/heads/master","pushedAt":"2023-08-30T23:21:14.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"HarkiratSohi","name":null,"path":"/HarkiratSohi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/116124471?s=80&v=4"},"commit":{"message":"Update README.md","shortMessageHtmlLink":"Update README.md"}},{"before":"aa365f756d54514c8e8eca5bce6459b746691d5a","after":"e910580a9b1dfec16f51fbc12073c513a242bf67","ref":"refs/heads/master","pushedAt":"2023-08-30T23:16:42.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"HarkiratSohi","name":null,"path":"/HarkiratSohi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/116124471?s=80&v=4"},"commit":{"message":"Added functionality log2 transforming the data if not already transformed","shortMessageHtmlLink":"Added functionality log2 transforming the data if not already transfo…"}},{"before":"356a52cb9d67567c7ba713b4ade48ee20ec7370d","after":"aa365f756d54514c8e8eca5bce6459b746691d5a","ref":"refs/heads/master","pushedAt":"2023-08-30T20:30:20.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"HarkiratSohi","name":null,"path":"/HarkiratSohi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/116124471?s=80&v=4"},"commit":{"message":"Updated files & documentation using devtools::document()","shortMessageHtmlLink":"Updated files & documentation using devtools::document()"}},{"before":"6dc1d0aac843c270819f060a4ce2869da3127144","after":"356a52cb9d67567c7ba713b4ade48ee20ec7370d","ref":"refs/heads/master","pushedAt":"2023-08-30T19:21:57.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"HarkiratSohi","name":null,"path":"/HarkiratSohi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/116124471?s=80&v=4"},"commit":{"message":"Update volcanoPlot_DiffExSpe.R\n\nRemoved unused parameter ylab","shortMessageHtmlLink":"Update volcanoPlot_DiffExSpe.R"}},{"before":"60c09b795ea2e6b0266c58ff5b2354068c1266c0","after":"6dc1d0aac843c270819f060a4ce2869da3127144","ref":"refs/heads/master","pushedAt":"2023-08-30T18:57:55.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"HarkiratSohi","name":null,"path":"/HarkiratSohi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/116124471?s=80&v=4"},"commit":{"message":"Update volcanoPlot_DiffExSpe.R\n\nAdded the pval_corrected boolean input parameter","shortMessageHtmlLink":"Update volcanoPlot_DiffExSpe.R"}},{"before":"586e6bc4691b2f5ca471c6ee4210a9de65e8dcb8","after":"60c09b795ea2e6b0266c58ff5b2354068c1266c0","ref":"refs/heads/master","pushedAt":"2023-08-29T21:07:03.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"HarkiratSohi","name":null,"path":"/HarkiratSohi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/116124471?s=80&v=4"},"commit":{"message":"Merge pull request #17 from PNNL-CompBio/fix-spatialDiffEx-oneCategoryVsAllOthers\n\nFixed spatialDiffEx.R\r\nFixed the line of code that defines samp2 for the case of comparing one category of samples vs. all others. Difference (setDiff) should be based on nrow, not ncol of colData(spe).","shortMessageHtmlLink":"Merge pull request #17 from PNNL-CompBio/fix-spatialDiffEx-oneCategor…"}},{"before":"586e6bc4691b2f5ca471c6ee4210a9de65e8dcb8","after":"4bca3a3a816d2c94523aa2971570ec10963e47cb","ref":"refs/heads/fix-spatialDiffEx-oneCategoryVsAllOthers","pushedAt":"2023-08-29T21:05:09.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"HarkiratSohi","name":null,"path":"/HarkiratSohi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/116124471?s=80&v=4"},"commit":{"message":"Update spatialDiffEx.R\n\nFixed the line of code that defines samp2 for the case of comparing one category of samples vs. all others. Difference (setDiff) should be based on nrow, not ncol of colData(spe).","shortMessageHtmlLink":"Update spatialDiffEx.R"}},{"before":null,"after":"586e6bc4691b2f5ca471c6ee4210a9de65e8dcb8","ref":"refs/heads/fix-spatialDiffEx-oneCategoryVsAllOthers","pushedAt":"2023-08-29T21:01:13.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"HarkiratSohi","name":null,"path":"/HarkiratSohi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/116124471?s=80&v=4"},"commit":{"message":"Update spatialDiffEx.R\n\nUpdated description of the parameter compare_vals","shortMessageHtmlLink":"Update spatialDiffEx.R"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEKE9lygA","startCursor":null,"endCursor":null}},"title":"Activity · PNNL-CompBio/spammR"}