Bioconductor Code: Browse

Graph of singleCellTK

446872041 (HEAD -> master, origin/master, origin/HEAD) bump x.y.z version to odd y following creation of RELEASE_3_16 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2022-11-01 11:17:41 -0400;
711d2ed92 (origin/RELEASE_3_16, RELEASE_3_16) bump x.y.z version to even y prior to creation of RELEASE_3_16 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2022-11-01 11:17:41 -0400;
8a7dfffb5 New version 2.7.3 by Yichen Wang <wangych@bu.edu> 2022-10-25 16:23:57 -0400;
2dc20e564 Update SingleR unit tests so it works for all versions of SingleR by Yichen Wang <wangych@bu.edu> 2022-10-25 12:21:01 -0400;
7730f3bd5 Fix SingleR requirement by Yichen Wang <wangych@bu.edu> 2022-10-25 11:53:38 -0400;
bc3b5e28b Fix CHECK errors due to SingleR updates by Yichen Wang <wangych@bu.edu> 2022-10-25 11:39:08 -0400;
a76fffb1d update docs by Yichen Wang <wangych@bu.edu> 2022-10-20 17:17:51 -0400;
261e0bc62 Merge branch 'devel' of https://github.com/mvfki/singleCellTK into devel by Yichen Wang <wangych@bu.edu> 2022-10-20 16:50:50 -0400;
c91787504 New version number; rebuilt docs; fixed QC UI bugs by Yichen Wang <wangych@bu.edu> 2022-10-20 16:04:38 -0400;
81755af90 New version number; rebuilt docs; fixed QC UI bugs by Yichen Wang <wangych@bu.edu> 2022-10-20 16:04:38 -0400;
7a8ed9310 Fixed BiocCheck warning related to 'require' by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-10-19 21:10:27 -0400;
41b3c78de Merge pull request <a href="#639">#639</a> from salzcamino/master by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-10-19 14:55:56 -0400;
ce01b556f update vam documentation by salzcamino <salamha@bu.edu> 2022-10-19 14:15:03 -0400;
42070d5c2 vam documentation by salzcamino <salamha@bu.edu> 2022-10-19 13:31:24 -0400;
d4c229edb Merge branch 'master' of https://github.com/salzcamino/singleCellTK by salzcamino <salamha@bu.edu> 2022-10-19 11:00:10 -0400;
0f75a92c9 change VAM defaults by salzcamino <salamha@bu.edu> 2022-10-19 11:00:00 -0400;
ab261db57 Merge pull request <a href="#40">#40</a> from compbiomed/devel by Salam AlAbdullatif <salamha@bu.edu> 2022-10-19 17:59:20 +0300;
51c7ffaf8 Merge branch 'master' of https://github.com/salzcamino/singleCellTK by salzcamino <salamha@bu.edu> 2022-10-19 10:57:26 -0400;
0f72a11fd remove do.call (hanging issue) by salzcamino <salamha@bu.edu> 2022-10-19 10:56:50 -0400;
7225786f9 Merge pull request <a href="#638">#638</a> from mvfki/devel by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-10-19 08:23:06 -0400;
fe559800d Fix check error by Yichen Wang <wangych@bu.edu> 2022-10-18 15:29:41 +0800;
9845cd6e6 Disable harmony example for now by Yichen Wang <wangych@bu.edu> 2022-10-18 01:56:13 +0800;
2d9a1c96f Fix combineSCE related SCTK_QC pipeline by Yichen Wang <wangych@bu.edu> 2022-10-17 15:25:02 +0800;
229625bd3 Update barcodeRank and EmptyDrops by Yichen Wang <wangych@bu.edu> 2022-10-14 17:54:10 +0800;
c97e881e1 Update DoubletFinder by Yichen Wang <wangych@bu.edu> 2022-10-14 15:23:28 +0800;
b0170764a Update scrublet by Yichen Wang <wangych@bu.edu> 2022-10-13 02:45:06 +0800;
dc098aeff fix by Yichen Wang <wangych@bu.edu> 2022-10-12 16:53:14 +0800;
3f814b576 Update bcds and cxds by Yichen Wang <wangych@bu.edu> 2022-10-12 16:52:32 +0800;
99c624c82 Update ScDblFinder for consistent metadata structure & runQuickUMAP bug fix by Yichen Wang <wangych@bu.edu> 2022-10-12 12:11:02 +0800;
b3546bc28 Update runPerCellQC() for consistent metadata structure by Yichen Wang <wangych@bu.edu> 2022-10-12 10:40:38 +0800;
6d623a320 Merge pull request <a href="#39">#39</a> from compbiomed/devel by Salam AlAbdullatif <salamha@bu.edu> 2022-10-11 16:09:46 +0300;
ea30e813b Merge pull request <a href="#629">#629</a> from mvfki/devel by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-10-04 15:06:05 -0400;
da312b1ad Merge pull request <a href="#627">#627</a> from salzcamino/master by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-10-04 11:33:59 -0400;
bebc0f3f3 Fix some UI bugs by Yichen Wang <wangych@bu.edu> 2022-10-04 10:50:20 +0800;
3f91c493b Update HVG method param by salzcamino <salamha@bu.edu> 2022-10-03 14:37:40 -0400;
f86a5ad97 update plotFindMarkerHeatmap name by salzcamino <salamha@bu.edu> 2022-10-03 14:25:20 -0400;
909a99aa6 Merge branch 'master' of https://github.com/salzcamino/singleCellTK by salzcamino <salamha@bu.edu> 2022-10-03 14:00:00 -0400;
5a1a7281c skipSoupX_bg fix by salzcamino <salamha@bu.edu> 2022-10-03 13:42:37 -0400;
e3181d83c Merge pull request <a href="#38">#38</a> from compbiomed/devel by Salam AlAbdullatif <salamha@bu.edu> 2022-10-03 15:04:26 +0300;
252338de9 Merge pull request <a href="#626">#626</a> from irzamsarfraz/devel by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-10-01 16:55:20 -0400;
e0df18045 importSTARSolo now looks for metrics in either Gene or GeneFull folders <a href="#616">#616</a> by Irzam Sarfraz <irzam9095@gmail.com> 2022-10-01 13:16:08 -0400;
71984ccf5 Fix as(., "dgCMatrix") issue, note that SoupX is still failing by Yichen Wang <wangych@bu.edu> 2022-09-30 12:09:54 +0800;
b30e7839e Merge pull request <a href="#37">#37</a> from compbiomed/devel by Salam AlAbdullatif <salamha@bu.edu> 2022-09-29 21:32:03 +0300;
69a75c0b8 Merge pull request <a href="#622">#622</a> from mvfki/devel by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-09-29 12:28:57 -0400;
ae4bffec6 Fix R CMD CHECK warning by Yichen Wang <wangych@bu.edu> 2022-09-29 16:58:00 +0800;
382b88e5b Fix UI filtering bug by Yichen Wang <wangych@bu.edu> 2022-09-29 16:02:27 +0800;
8efa718ce Minor bug fix by Yichen Wang <wangych@bu.edu> 2022-09-29 11:02:28 +0800;
8b21d3759 Fix Rd man warnings by Yichen Wang <wangych@bu.edu> 2022-09-29 11:01:51 +0800;
52a034977 Minor bug fix for runFindMarker by Yichen Wang <wangych@bu.edu> 2022-09-29 09:19:48 +0800;
15ee8bf0d Update runUMAP, runTSNE in other parts of the toolkit by Yichen Wang <wangych@bu.edu> 2022-09-28 15:23:08 +0800;
27e3c620f Deprecate `getTSNE`, add `runTSNE` and `runQuickTSNE` by Yichen Wang <wangych@bu.edu> 2022-09-28 14:39:03 +0800;
c35af4eb2 Deprecate "getUMAP", add "runUMAP" and "runQuickUMAP" by Yichen Wang <wangych@bu.edu> 2022-09-28 11:49:28 +0800;
55b540478 Fix the default arguments for in Cell QC RMD report by Yichen Wang <wangych@bu.edu> 2022-09-27 22:43:15 +0800;
6ed94a827 Merge pull request <a href="#621">#621</a> from mvfki/devel by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-09-23 10:43:31 -0400;
89631c60a Fix CHECK issues by Yichen Wang <wangych@wangyichendeMacBook-Air.local> 2022-09-23 12:25:14 +0800;
1c1220da5 Minor update to plotting func for element size adjustment by mvfki <wangych@bu.edu> 2022-09-23 11:33:27 +0800;
574d9dbfb Merge pull request <a href="#36">#36</a> from compbiomed/devel by Salam AlAbdullatif <salamha@bu.edu> 2022-09-14 16:45:42 +0300;
56d97c1cb Merge pull request <a href="#618">#618</a> from mvfki/devel by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-09-10 22:24:11 -0400;
484514933 Bug fix by mvfki <wangych@bu.edu> 2022-09-10 13:43:58 +0800;
800d2b97c Merge pull request <a href="#614">#614</a> from mvfki/devel by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-09-09 11:47:22 -0400;
ef608c1ef Finish up heatmap updates by Yichen Wang <wangych@bu.edu> 2022-09-08 09:41:38 +0800;
06075a219 fix cluster summary by salzcamino <salamha@bu.edu> 2022-08-26 09:49:07 -0400;
84664fd78 Refactor plotSCEHeatmap (halfway) by Yichen Wang <wangych@bu.edu> 2022-08-17 19:08:51 -0400;
b2ca29493 Add detectThresh for runFindMarker by Yichen Wang <wangych@bu.edu> 2022-08-11 16:31:20 -0400;
b18779165 Deprecate old findMarker function names by Yichen Wang <wangych@bu.edu> 2022-08-11 16:00:51 -0400;
5fb2ad899 Merge branch 'devel' of https://github.com/compbiomed/singleCellTK into devel by Yichen Wang <wangych@bu.edu> 2022-08-11 12:49:50 -0400;
93e2414e0 Add .selectSCEMatrix() and .manageCellVar; together with refining batch correction functions by Yichen Wang <wangych@bu.edu> 2022-08-11 12:49:05 -0400;
8d42e0185 Merge pull request <a href="#610">#610</a> from npervaiz/devel by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-08-04 08:06:28 -0400;
4957169e9 bugs fixed by nida pervaiz <nidapervaiz27@gmail.com> 2022-08-01 19:30:49 +0200;
8ddcd1776 changes reverted back by nida pervaiz <nidapervaiz27@gmail.com> 2022-08-01 17:57:04 +0200;
ffe2f79eb fishpond replaced with eds by nida pervaiz <nidapervaiz27@gmail.com> 2022-08-01 17:27:11 +0200;
2599ca7fe modular update in findMarker function by nida pervaiz <nidapervaiz27@gmail.com> 2022-08-01 17:20:57 +0200;
a34d63a2c Add harmony for batch correction by Yichen Wang <wangych@bu.edu> 2022-07-15 21:03:49 -0400;
75d89510d Update DE report by Yichen Wang <wangych@bu.edu> 2022-07-15 12:06:40 -0400;
4b263d957 Merge branch 'devel' of https://github.com/compbiomed/singleCellTK into devel by Yichen Wang <wangych@bu.edu> 2022-06-30 15:47:04 -0400;
99e76b9c3 Add master branch to GitHub Action workflows by Yichen Wang <wangych@bu.edu> 2022-06-30 14:32:34 -0400;
c22dbbf9c Fix CHECK warning by Yichen Wang <wangych@bu.edu> 2022-06-30 11:24:27 -0400;
2f1fa6bff Fix CHECK warning by Yichen Wang <wangych@bu.edu> 2022-06-30 10:50:21 -0400;
58223dcad Fix CHECK warning by Yichen Wang <wangych@bu.edu> 2022-06-29 20:29:14 -0400;
7d46c6eb7 new version 2.7.1 by Yichen Wang <wangych@bu.edu> 2022-06-29 19:30:51 -0400;
f0b0d74b6 Fix check errors by Yichen Wang <wangych@bu.edu> 2022-06-28 18:07:14 -0400;
fc7a1024b Fix README by Yichen Wang <wangych@bu.edu> 2022-06-28 16:52:12 -0400;
976db8699 Added more unit tests by Yichen Wang <wangych@bu.edu> 2022-06-28 16:51:30 -0400;
cb664b173 Merge remote-tracking branch 'bioc/master' into devel by Yichen Wang <wangych@bu.edu> 2022-06-28 11:58:58 -0400;
f8d73fc72 Merge pull request <a href="#602">#602</a> from mvfki/devel by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-06-27 10:45:11 -0400;
2b06c0eeb roxygen by Yichen Wang <wangych@bu.edu> 2022-06-25 18:18:49 -0400;
2f8d6a0ef Update documentation, together with minor bug fixes by Yichen Wang <wangych@bu.edu> 2022-06-25 17:35:08 -0400;
b8cd44998 Update documentation of workflow related to new HVG and scaling scheme by Yichen Wang <wangych@bu.edu> 2022-06-23 17:59:06 -0400;
18a0f0e66 Fix CHECK and BiocCheck by Yichen Wang <wangych@bu.edu> 2022-06-23 10:38:52 -0400;
408838a08 upgrade R 4.2.0 by Yichen Wang <wangych@bu.edu> 2022-06-22 21:49:13 -0400;
bf4524f08 Refine changes previously made, and minor bug fixes by Yichen Wang <wangych@bu.edu> 2022-06-22 16:55:48 -0400;
d3b410fce Update UI according to the last commit by Yichen Wang <wangych@bu.edu> 2022-06-18 08:35:21 -0400;
007a2c8d7 Efficiency and user experience improvement & BUG fixes for TSCAN workflow by Yichen Wang <wangych@bu.edu> 2022-06-16 14:54:41 -0400;
497cbfb4a Reformat the use of withConsoleMastRedirect; A few UI bug fixes by Yichen Wang <wangych@bu.edu> 2022-06-14 13:30:54 -0400;
d401387bc Merge branch 'devel' of https://github.com/compbiomed/singleCellTK into devel by Yichen Wang <wangych@bu.edu> 2022-06-12 11:04:58 -0400;
fadfb773d Minor UI fixes by Yichen Wang <wangych@bu.edu> 2022-06-12 11:03:33 -0400;
b0f8638d1 Merge pull request <a href="#600">#600</a> from npervaiz/devel by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-06-11 17:40:49 -0400;
388b4b98b minor tweak fixed by nida pervaiz <nidapervaiz27@gmail.com> 2022-06-10 11:28:31 +0200;
cc19b5c6d Merge branch 'devel' of https://github.com/npervaiz/singleCellTK into devel by nida pervaiz <nidapervaiz27@gmail.com> 2022-06-10 10:55:45 +0200;
9f17a6fbf Import data UI modified by nida pervaiz <nidapervaiz27@gmail.com> 2022-06-10 10:55:33 +0200;