| ccedee1 | Luke Zappia | 30 January 2023, 10:06:52 UTC | Merge pull request #161 from azodichr/issue-158 Fixes #158, fixes #160 | 30 January 2023, 10:06:52 UTC |
| aa4d505 | Luke Zappia | 30 January 2023, 10:04:40 UTC | Bump version and update NEWS | 30 January 2023, 10:04:40 UTC |
| 6e00a8e | cazodi | 27 January 2023, 16:53:18 UTC | address bug with conditional group assignements being incorrect in cases where batch effects are applied. See issues 158 and 160. | 27 January 2023, 16:53:18 UTC |
| 4ae4461 | Christina Del Azodi | 25 January 2023, 14:37:20 UTC | Merge pull request #1 from Oshlack/master Pulling most recent version of splatter for issue fixing | 25 January 2023, 14:37:20 UTC |
| 7f6a3d4 | Luke Zappia | 04 November 2022, 12:51:36 UTC | Bioconductor 3.17 devel | 04 November 2022, 12:51:53 UTC |
| bf4e5bd | Luke Zappia | 04 November 2022, 12:51:09 UTC | Merge remote-tracking branch 'upstream/master' * upstream/master: bump x.y.z version to odd y following creation of RELEASE_3_16 branch | 04 November 2022, 12:51:09 UTC |
| 0f0f170 | Luke Zappia | 04 November 2022, 12:46:06 UTC | Bioconductor 3.16 release | 04 November 2022, 12:46:06 UTC |
| 851704e | Luke Zappia | 04 November 2022, 12:44:56 UTC | Merge remote-tracking branch 'upstream/RELEASE_3_16' * upstream/RELEASE_3_16: bump x.y.z version to even y prior to creation of RELEASE_3_16 branch | 04 November 2022, 12:44:56 UTC |
| 5c0f8ec | J Wokaty | 01 November 2022, 15:15:07 UTC | bump x.y.z version to even y prior to creation of RELEASE_3_16 branch | 01 November 2022, 15:15:07 UTC |
| 5c9c642 | J Wokaty | 01 November 2022, 15:15:07 UTC | bump x.y.z version to odd y following creation of RELEASE_3_16 branch | 01 November 2022, 15:15:07 UTC |
| 1768d11 | Luke Zappia | 26 October 2022, 20:14:21 UTC | Update NEWS for Bioconductor 3.16 release | 26 October 2022, 20:14:21 UTC |
| 32a0c0b | Luke Zappia | 26 October 2022, 20:10:16 UTC | Bump version and update NEWS | 26 October 2022, 20:10:16 UTC |
| e27abb1 | Luke Zappia | 26 October 2022, 20:04:07 UTC | Update GitHub Actions workflow (#155) | 26 October 2022, 20:04:07 UTC |
| 8e11de4 | Luke Zappia | 26 October 2022, 20:01:28 UTC | Merge pull request #151 from azodichr/issue_149 Fixes #149 | 26 October 2022, 20:01:28 UTC |
| 385e537 | Luke Zappia | 25 October 2022, 12:42:36 UTC | Remove extra set.seed() calls in splatPopSimulate() | 25 October 2022, 12:42:36 UTC |
| 5e3fff7 | Luke Zappia | 25 October 2022, 12:41:43 UTC | Add test that SplatPop seeds are reproducible | 25 October 2022, 12:41:43 UTC |
| 82700d5 | Luke Zappia | 25 October 2022, 12:30:14 UTC | Add test for different cell numbers in splatPopSimulate() When nCells.sample=TRUE | 25 October 2022, 12:30:14 UTC |
| e239f82 | cazodi | 13 October 2022, 14:55:09 UTC | fix bug where the same nCells was being sampled for each donor | 13 October 2022, 14:55:09 UTC |
| 4bdac02 | Luke Zappia | 10 October 2022, 09:41:32 UTC | Adjust styling | 10 October 2022, 09:41:32 UTC |
| f06f4e6 | Luke Zappia | 10 October 2022, 09:08:56 UTC | Resolve minor comments | 10 October 2022, 09:08:56 UTC |
| 3a0f014 | Luke Zappia | 10 October 2022, 08:40:07 UTC | Bump roxygen version and reoxygenise | 10 October 2022, 08:40:07 UTC |
| d6a5d4c | Luke Zappia | 11 August 2022, 13:13:53 UTC | Fix bug in BASiCSSimulate() when spike.means is resampled Fixes #153 | 11 August 2022, 13:13:53 UTC |
| b586283 | cazodi | 22 July 2022, 18:48:09 UTC | fix nCells samper when only one batch is being simulated | 22 July 2022, 18:48:09 UTC |
| 23268a6 | cazodi | 21 July 2022, 20:11:37 UTC | fix Row.names vs rownames bug and catch batch.size request mistakes | 21 July 2022, 20:11:37 UTC |
| a963d8d | Luke Zappia | 28 April 2022, 13:18:31 UTC | Bioconductor 3.16 devel | 28 April 2022, 13:18:31 UTC |
| 795c624 | Luke Zappia | 28 April 2022, 13:17:52 UTC | Merge remote-tracking branch 'upstream/master' * upstream/master: bump x.y.z version to odd y following creation of RELEASE_3_15 branch | 28 April 2022, 13:17:52 UTC |
| d56ae77 | Luke Zappia | 28 April 2022, 13:07:04 UTC | Bioconductor 3.15 release | 28 April 2022, 13:07:04 UTC |
| 9a33847 | Luke Zappia | 28 April 2022, 13:05:03 UTC | Merge remote-tracking branch 'upstream/RELEASE_3_15' * upstream/RELEASE_3_15: bump x.y.z version to even y prior to creation of RELEASE_3_15 branch | 28 April 2022, 13:05:03 UTC |
| 69f3f4b | Nitesh Turaga | 26 April 2022, 15:38:40 UTC | bump x.y.z version to odd y following creation of RELEASE_3_15 branch | 26 April 2022, 15:38:40 UTC |
| e60b5a4 | Nitesh Turaga | 26 April 2022, 15:38:40 UTC | bump x.y.z version to even y prior to creation of RELEASE_3_15 branch | 26 April 2022, 15:38:40 UTC |
| 14963a6 | Luke Zappia | 25 April 2022, 08:26:58 UTC | Update NEWS.Rd for release | 25 April 2022, 08:26:58 UTC |
| 06668c9 | Luke Zappia | 23 April 2022, 08:12:19 UTC | Add starting point for dropout fit estimation Borrowed from InferCNV | 23 April 2022, 08:12:19 UTC |
| 8994c43 | Luke Zappia | 11 March 2022, 14:22:06 UTC | Merge pull request #134 from wenjie2wang/issue-132 Fixes #132 | 11 March 2022, 14:22:06 UTC |
| a1784c4 | Luke Zappia | 11 March 2022, 14:19:41 UTC | Bump devel version Fixes #132 | 11 March 2022, 14:19:41 UTC |
| e3aa46e | Luke Zappia | 11 March 2022, 14:16:55 UTC | Manually assign SCdat in newSCDDParams() Old method didn't work with new initalize method | 11 March 2022, 14:16:55 UTC |
| 8c27433 | Wenjie Wang | 08 March 2022, 02:52:01 UTC | Add testing examples for the initialize() method of Params | 08 March 2022, 02:52:01 UTC |
| 2a0db0a | Wenjie Wang | 08 March 2022, 02:51:15 UTC | Move the initialize() method to Params-methods.R with GH reference | 08 March 2022, 02:51:15 UTC |
| f539996 | Wenjie Wang | 28 January 2022, 18:31:17 UTC | Use initialize() method instead of prototype for Params class See issue #132 | 28 January 2022, 18:31:17 UTC |
| 1eec243 | Luke Zappia | 28 January 2022, 12:06:47 UTC | Add port method to splatEstDropout Fixes #133 | 28 January 2022, 12:06:47 UTC |
| 1f95b61 | Luke Zappia | 28 January 2022, 11:05:49 UTC | Removed duplicated code in splatSimPathCellMeans() Fixes #131 | 28 January 2022, 11:06:53 UTC |
| 3a9274c | Luke Zappia | 10 January 2022, 18:04:09 UTC | Merge branch 'master' of github.com:Oshlack/splatter * 'master' of github.com:Oshlack/splatter: | 10 January 2022, 18:04:09 UTC |
| 94a74a2 | Luke Zappia | 10 January 2022, 17:57:29 UTC | Merge branch 'master' of github.com:Oshlack/splatter * 'master' of github.com:Oshlack/splatter: Added citation and link to vignette for splatPop Adjust NEWS Update NEWS Fixed bug 125 where the conditional QTL effects were being divided among all donors instead of by donor condition group Bioconductor 3.15 devel Bioconductor 3.14 release bump x.y.z version to odd y following creation of RELEASE_3_14 branch | 10 January 2022, 18:02:37 UTC |
| a0d25ac | Luke Zappia | 10 January 2022, 17:57:29 UTC | Merge branch 'master' of github.com:Oshlack/splatter * 'master' of github.com:Oshlack/splatter: Added citation and link to vignette for splatPop Adjust NEWS Update NEWS Fixed bug 125 where the conditional QTL effects were being divided among all donors instead of by donor condition group Bioconductor 3.15 devel Bioconductor 3.14 release bump x.y.z version to odd y following creation of RELEASE_3_14 branch | 10 January 2022, 17:57:29 UTC |
| 675403c | Luke Zappia | 10 January 2022, 17:47:54 UTC | Bump release version | 10 January 2022, 17:54:31 UTC |
| 5580e17 | Luke Zappia | 10 January 2022, 17:28:02 UTC | Bump version | 10 January 2022, 17:54:12 UTC |
| e17bcbb | Luke Zappia | 10 January 2022, 17:21:08 UTC | Fix scran dependency in lun2Estimate() Also added a basic test Fixes #130 | 10 January 2022, 17:53:17 UTC |
| 00490ea | Luke Zappia | 10 January 2022, 13:43:04 UTC | Update preprint DOIs in listSims() | 10 January 2022, 17:53:17 UTC |
| 6e1fed9 | Luke Zappia | 10 January 2022, 13:38:53 UTC | Add splatPop DOI to listSims() | 10 January 2022, 17:53:17 UTC |
| e26a42f | Luke Zappia | 10 January 2022, 13:37:07 UTC | Add note about citing models to CITATION | 10 January 2022, 17:53:17 UTC |
| 20dc9be | Christina Azodi | 20 December 2021, 06:15:21 UTC | Added citation and link to vignette for splatPop | 10 January 2022, 17:53:17 UTC |
| 2d55643 | Luke Zappia | 02 November 2021, 10:29:40 UTC | Adjust NEWS | 10 January 2022, 17:53:17 UTC |
| 4771642 | Luke Zappia | 02 November 2021, 10:17:29 UTC | Update NEWS | 10 January 2022, 17:53:17 UTC |
| 01f06d3 | cazodi | 26 October 2021, 23:28:55 UTC | Fixed bug 125 where the conditional QTL effects were being divided among all donors instead of by donor condition group | 10 January 2022, 17:53:17 UTC |
| 403b181 | Luke Zappia | 02 November 2021, 10:03:39 UTC | Bioconductor 3.15 devel | 10 January 2022, 17:53:17 UTC |
| b0881a8 | Nitesh Turaga | 26 October 2021, 16:32:42 UTC | bump x.y.z version to odd y following creation of RELEASE_3_14 branch | 10 January 2022, 17:53:12 UTC |
| 0453e39 | Luke Zappia | 02 November 2021, 09:53:41 UTC | Bioconductor 3.14 release | 10 January 2022, 17:51:25 UTC |
| d505d1d | Luke Zappia | 10 January 2022, 13:51:02 UTC | Merge pull request #129 from azodichr/master | 10 January 2022, 13:51:02 UTC |
| 1246a9b | Christina Azodi | 20 December 2021, 06:15:21 UTC | Added citation and link to vignette for splatPop | 20 December 2021, 06:15:21 UTC |
| 40e2421 | Luke Zappia | 02 November 2021, 10:30:18 UTC | Merge branch 'RELEASE_3_14' * RELEASE_3_14: Adjust NEWS | 02 November 2021, 10:32:13 UTC |
| aeb27ea | Luke Zappia | 02 November 2021, 10:29:40 UTC | Adjust NEWS | 02 November 2021, 10:29:40 UTC |
| 4a6eb12 | Luke Zappia | 02 November 2021, 10:28:38 UTC | Merge branch 'bugfix_125' into RELEASE_3_14 * bugfix_125: Update NEWS Fixed bug 125 where the conditional QTL effects were being divided among all donors instead of by donor condition group Bioconductor 3.15 devel Bioconductor 3.14 release bump x.y.z version to odd y following creation of RELEASE_3_14 branch | 02 November 2021, 10:28:38 UTC |
| 540b80a | Luke Zappia | 02 November 2021, 10:17:53 UTC | Merge branch 'bugfix_125' Fixes #125 * bugfix_125: Update NEWS Fixed bug 125 where the conditional QTL effects were being divided among all donors instead of by donor condition group | 02 November 2021, 10:17:53 UTC |
| b381902 | Luke Zappia | 02 November 2021, 10:17:29 UTC | Update NEWS | 02 November 2021, 10:17:29 UTC |
| 27396df | cazodi | 26 October 2021, 23:28:55 UTC | Fixed bug 125 where the conditional QTL effects were being divided among all donors instead of by donor condition group | 02 November 2021, 10:13:14 UTC |
| 9cb8fe9 | Luke Zappia | 02 November 2021, 10:03:39 UTC | Bioconductor 3.15 devel | 02 November 2021, 10:03:39 UTC |
| e40d106 | Luke Zappia | 02 November 2021, 10:02:51 UTC | Merge remote-tracking branch 'upstream/master' * upstream/master: bump x.y.z version to odd y following creation of RELEASE_3_14 branch | 02 November 2021, 10:02:51 UTC |
| 6dd25b8 | Luke Zappia | 02 November 2021, 09:53:41 UTC | Bioconductor 3.14 release | 02 November 2021, 09:53:41 UTC |
| 5e5d9ba | Luke Zappia | 02 November 2021, 09:50:59 UTC | Merge remote-tracking branch 'upstream/RELEASE_3_14' * upstream/RELEASE_3_14: bump x.y.z version to even y prior to creation of RELEASE_3_14 branch | 02 November 2021, 09:50:59 UTC |
| 2a816ed | Nitesh Turaga | 26 October 2021, 16:32:42 UTC | bump x.y.z version to even y prior to creation of RELEASE_3_14 branch | 26 October 2021, 16:32:42 UTC |
| f119d86 | Nitesh Turaga | 26 October 2021, 16:32:42 UTC | bump x.y.z version to odd y following creation of RELEASE_3_14 branch | 26 October 2021, 16:32:42 UTC |
| 58bb6c9 | Luke Zappia | 22 October 2021, 08:10:18 UTC | Prep for release | 22 October 2021, 08:10:18 UTC |
| 4edfb8b | Luke Zappia | 07 October 2021, 12:13:30 UTC | Update NEWS | 07 October 2021, 12:13:30 UTC |
| 6515aee | Luke Zappia | 07 October 2021, 12:05:59 UTC | Improve SplatParams group.prob checks Fixes #107 | 07 October 2021, 12:05:59 UTC |
| b893c4f | Luke Zappia | 06 October 2021, 08:23:06 UTC | Merge pull request #123 from azodichr/splatPop_updates | 06 October 2021, 08:23:06 UTC |
| 26bb0d7 | Luke Zappia | 06 October 2021, 08:22:17 UTC | Update date in DESCRIPTION | 06 October 2021, 08:22:17 UTC |
| a24a221 | cazodi | 05 October 2021, 23:44:29 UTC | addressing Lukes comments from 4 Oct 2021 | 05 October 2021, 23:44:29 UTC |
| a79c18c | cazodi | 28 September 2021, 06:16:58 UTC | clean up updates for next release | 28 September 2021, 06:16:58 UTC |
| f37eae4 | cazodi | 01 September 2021, 06:37:09 UTC | fix bug with too many cells being simulated when simulating multiple batches | 01 September 2021, 06:37:09 UTC |
| 37148b8 | cazodi | 19 August 2021, 05:38:46 UTC | added function to simulate coregulated genes with eqtl.coreg | 19 August 2021, 05:38:46 UTC |
| 2d68217 | cazodi | 19 August 2021, 05:36:19 UTC | added function to simulate coregulated genes with eqtl.coreg | 19 August 2021, 05:36:19 UTC |
| 7050593 | cazodi | 17 August 2021, 04:30:16 UTC | first test new function to simulate directly from empirical vcf, eQTL mapping data, and population gene means | 17 August 2021, 04:30:16 UTC |
| 273ecf1 | cazodi | 12 August 2021, 07:40:10 UTC | fixed cell name duplication bug | 12 August 2021, 07:40:10 UTC |
| bef776a | Luke Zappia | 20 May 2021, 08:38:13 UTC | Merge branch 'RELEASE_3_13' * RELEASE_3_13: Fix bug in validating splatPopParams | 20 May 2021, 08:38:13 UTC |
| 62da653 | Luke Zappia | 20 May 2021, 08:36:12 UTC | Fix bug in validating splatPopParams | 20 May 2021, 08:36:12 UTC |
| 1cf6943 | Luke Zappia | 20 May 2021, 08:31:48 UTC | Biconductor 3.14 devel | 20 May 2021, 08:31:48 UTC |
| de929df | Luke Zappia | 20 May 2021, 08:30:59 UTC | Merge remote-tracking branch 'upstream/master' * upstream/master: bump x.y.z version to odd y following creation of RELEASE_3_13 branch | 20 May 2021, 08:30:59 UTC |
| 27a2fd7 | Luke Zappia | 20 May 2021, 08:24:37 UTC | Merge branch 'RELEASE_3_13' * RELEASE_3_13: Update NEWS for Bioconductor 3.13 bump x.y.z version to even y prior to creation of RELEASE_3_13 branch | 20 May 2021, 08:24:37 UTC |
| b122dbd | Luke Zappia | 20 May 2021, 08:22:15 UTC | Update NEWS for Bioconductor 3.13 | 20 May 2021, 08:22:15 UTC |
| 2157ddd | Nitesh Turaga | 19 May 2021, 16:25:33 UTC | bump x.y.z version to even y prior to creation of RELEASE_3_13 branch | 19 May 2021, 16:25:33 UTC |
| fcc1d80 | Nitesh Turaga | 19 May 2021, 16:25:33 UTC | bump x.y.z version to odd y following creation of RELEASE_3_13 branch | 19 May 2021, 16:25:33 UTC |
| 73a900f | Luke Zappia | 18 May 2021, 15:57:47 UTC | Update NEWS.Rd for release | 18 May 2021, 15:57:47 UTC |
| a3bcfb1 | Luke Zappia | 11 May 2021, 15:24:10 UTC | Adjust checking that vectors sum to 1 Fixes #107 | 11 May 2021, 15:24:10 UTC |
| d6adbdc | Luke Zappia | 11 May 2021, 15:23:34 UTC | Modify sparsifyMatrices() to handle logical matrices | 11 May 2021, 15:23:34 UTC |
| c8de659 | Luke Zappia | 11 May 2021, 14:17:56 UTC | Fix DESCRIPTION date | 11 May 2021, 14:17:56 UTC |
| 7a4c13a | Luke Zappia | 11 May 2021, 14:16:59 UTC | Merge pull request #113 from azodichr/splatPop_updates Alright, I think this is ready to merge 🎉. Thanks for addressing all my comments. There might be some small changes to make later on but let's see if it passes the Bioconductor checks first 🤞🏻. | 11 May 2021, 14:16:59 UTC |
| 6396e16 | Luke Zappia | 11 May 2021, 14:14:51 UTC | Update DESCRIPTION and NEWS | 11 May 2021, 14:14:51 UTC |
| d493749 | Luke Zappia | 11 May 2021, 14:07:05 UTC | Minor changes to tests to avoid #114 | 11 May 2021, 14:07:05 UTC |
| accdf18 | cazodi | 11 May 2021, 03:50:02 UTC | minor fixes suggested by luke | 11 May 2021, 03:50:02 UTC |
| 99db327 | Luke Zappia | 06 May 2021, 14:26:53 UTC | Fix vector argument name in expandParams() docs | 06 May 2021, 14:26:53 UTC |
| 3e11113 | cazodi | 04 May 2021, 07:09:38 UTC | fix issue with examples taking too long | 04 May 2021, 07:09:38 UTC |
