| 4018ddc | Luke Zappia | 06 May 2024, 11:40:26 UTC | Merge remote-tracking branch 'upstream/devel' into devel * upstream/devel: bump x.y.z version to odd y following creation of RELEASE_3_19 branch | 06 May 2024, 11:40:26 UTC |
| e081e7b | Luke Zappia | 06 May 2024, 11:32:33 UTC | Bioconductor 3.19 release | 06 May 2024, 11:32:33 UTC |
| f1f1c32 | Luke Zappia | 06 May 2024, 11:30:47 UTC | Merge remote-tracking branch 'upstream/RELEASE_3_19' into devel * upstream/RELEASE_3_19: bump x.y.z version to even y prior to creation of RELEASE_3_19 branch | 06 May 2024, 11:30:47 UTC |
| 5e5b43e | J Wokaty | 30 April 2024, 14:56:03 UTC | bump x.y.z version to even y prior to creation of RELEASE_3_19 branch | 30 April 2024, 14:56:03 UTC |
| bb957f9 | J Wokaty | 30 April 2024, 14:56:03 UTC | bump x.y.z version to odd y following creation of RELEASE_3_19 branch | 30 April 2024, 14:56:03 UTC |
| ff53275 | Luke Zappia | 23 April 2024, 10:54:34 UTC | Update NEWS for Bioconductor 3.19 release | 23 April 2024, 10:54:34 UTC |
| c2fe234 | Luke Zappia | 23 April 2024, 10:48:59 UTC | Set \dontrun for addGeneLengths example Avoid depending on annotation packages | 23 April 2024, 10:48:59 UTC |
| ea842a2 | Luke Zappia | 26 March 2024, 20:18:58 UTC | Update NEWS and bump version | 26 March 2024, 20:18:58 UTC |
| ed1afea | Luke Zappia | 26 March 2024, 20:09:59 UTC | Minor fixes from BiocCheck | 26 March 2024, 20:09:59 UTC |
| 8614ad6 | Luke Zappia | 26 March 2024, 19:53:25 UTC | Only ask to install dependencies when interactive | 26 March 2024, 19:53:25 UTC |
| 9472e2f | Luke Zappia | 26 March 2024, 19:50:23 UTC | Add @keywords internal/@noRd to function docs | 26 March 2024, 19:50:23 UTC |
| 81cf3e7 | Luke Zappia | 26 March 2024, 16:58:31 UTC | Restyle code Use something more modern/sane with styler::style_pkg(transformers = styler::tidyverse_style(indent_by = 4)) (and some adjusting) | 26 March 2024, 18:13:06 UTC |
| 31a9867 | Luke Zappia | 26 March 2024, 13:44:01 UTC | Update DESCRIPTION Add GitHub usernames and Bioconductor URL | 26 March 2024, 13:44:01 UTC |
| 411b3fa | Luke Zappia | 26 March 2024, 13:38:13 UTC | Replace package man page with usethis auto page | 26 March 2024, 13:38:13 UTC |
| ceac288 | Luke Zappia | 26 March 2024, 13:36:39 UTC | Bump roxygen version to 7.3.1 | 26 March 2024, 13:36:39 UTC |
| bd62c59 | Luke Zappia | 26 March 2024, 13:35:05 UTC | Specify expected warnings in tests Removes unhelpful output | 26 March 2024, 13:35:05 UTC |
| 7b8b13c | Luke Zappia | 26 March 2024, 13:22:31 UTC | Properly sink output in scDDSimulate() when verbose=FALSE | 26 March 2024, 13:22:31 UTC |
| 0454898 | Luke Zappia | 26 March 2024, 13:17:54 UTC | Set verbose=FALSE in tests for scDDSimulate() | 26 March 2024, 13:17:54 UTC |
| 1fb0eff | Luke Zappia | 26 March 2024, 13:17:27 UTC | Properly sink output in BASiCSEstimate when verbose=FALSE | 26 March 2024, 13:17:27 UTC |
| 220606e | Luke Zappia | 08 November 2023, 09:47:56 UTC | Merge remote-tracking branch 'upstream/devel' into devel * upstream/devel: bump x.y.z version to odd y following creation of RELEASE_3_18 branch | 08 November 2023, 09:47:56 UTC |
| aa4890b | Luke Zappia | 08 November 2023, 09:44:23 UTC | Bump version for 3.18 release | 08 November 2023, 09:44:23 UTC |
| 9694e99 | Luke Zappia | 08 November 2023, 09:43:19 UTC | Merge remote-tracking branch 'upstream/RELEASE_3_18' into devel * upstream/RELEASE_3_18: bump x.y.z version to even y prior to creation of RELEASE_3_18 branch | 08 November 2023, 09:43:19 UTC |
| 07e5c7d | J Wokaty | 24 October 2023, 14:55:11 UTC | bump x.y.z version to even y prior to creation of RELEASE_3_18 branch | 24 October 2023, 14:55:11 UTC |
| 616f085 | J Wokaty | 24 October 2023, 14:55:11 UTC | bump x.y.z version to odd y following creation of RELEASE_3_18 branch | 24 October 2023, 14:55:11 UTC |
| 3ee127b | Luke Zappia | 11 October 2023, 13:55:31 UTC | Fix bug in splatSimPathDE() DE factors are now adjusted for the originating path | 11 October 2023, 13:55:31 UTC |
| e253676 | Luke Zappia | 02 October 2023, 15:10:58 UTC | Update NEWS for release | 02 October 2023, 15:10:58 UTC |
| 569f213 | Luke Zappia | 02 May 2023, 12:20:00 UTC | Bioconductor 3.18 devel | 02 May 2023, 12:20:00 UTC |
| df05484 | Luke Zappia | 02 May 2023, 12:19:08 UTC | Merge remote-tracking branch 'upstream/devel' into devel * upstream/devel: bump x.y.z version to odd y following creation of RELEASE_3_17 branch | 02 May 2023, 12:19:08 UTC |
| dad2a3a | Luke Zappia | 02 May 2023, 12:13:51 UTC | Bioconductor 3.17 release | 02 May 2023, 12:13:51 UTC |
| 8898e93 | Luke Zappia | 02 May 2023, 12:12:27 UTC | Merge remote-tracking branch 'upstream/RELEASE_3_17' into devel * upstream/RELEASE_3_17: bump x.y.z version to even y prior to creation of RELEASE_3_17 branch | 02 May 2023, 12:12:27 UTC |
| e842966 | J Wokaty | 25 April 2023, 14:52:06 UTC | bump x.y.z version to odd y following creation of RELEASE_3_17 branch | 25 April 2023, 14:52:06 UTC |
| ee7a293 | J Wokaty | 25 April 2023, 14:52:06 UTC | bump x.y.z version to even y prior to creation of RELEASE_3_17 branch | 25 April 2023, 14:52:06 UTC |
| 6f97093 | Luke Zappia | 12 April 2023, 08:24:19 UTC | Replace ggplot2::aes_string() with ggplot2::aes() Fixes #75 | 12 April 2023, 08:24:19 UTC |
| bf80e83 | Luke Zappia | 12 April 2023, 07:57:51 UTC | Remove ggplot2 imports | 12 April 2023, 07:57:51 UTC |
| d247b17 | Luke Zappia | 10 April 2023, 17:15:48 UTC | Fix typo in DESCRIPTION | 10 April 2023, 17:15:48 UTC |
| 5606da0 | Luke Zappia | 05 April 2023, 14:09:59 UTC | Update GHA to use devel branch | 05 April 2023, 14:09:59 UTC |
| 64d0471 | Luke Zappia | 05 April 2023, 14:07:53 UTC | Merge branch 'seeds' into devel * seeds: Roxygenise Bump version Move ggplot2 to suggested Swap scater and scuttle dependencies | 05 April 2023, 14:07:53 UTC |
| fd39ff7 | Luke Zappia | 05 April 2023, 14:07:35 UTC | Roxygenise | 05 April 2023, 14:07:35 UTC |
| f3ae11b | Luke Zappia | 05 April 2023, 14:07:04 UTC | Bump version | 05 April 2023, 14:07:04 UTC |
| 2448cdc | Luke Zappia | 05 April 2023, 14:04:40 UTC | Move ggplot2 to suggested Save dependencies as plotting is not a core function | 05 April 2023, 14:04:40 UTC |
| 9b7d7aa | Luke Zappia | 05 April 2023, 13:55:47 UTC | Swap scater and scuttle dependencies Suggesting scater saves a few dependencies | 05 April 2023, 13:55:47 UTC |
| 597ad82 | Luke Zappia | 05 April 2023, 11:43:33 UTC | Update NEWS for Bioconductor 3.17 | 05 April 2023, 11:43:33 UTC |
| 8edc900 | Luke Zappia | 30 January 2023, 10:29:16 UTC | Merge branch 'RELEASE_3_16' * RELEASE_3_16: Bump version and update NEWS address bug with conditional group assignements being incorrect in cases where batch effects are applied. See issues 158 and 160. | 30 January 2023, 10:29:16 UTC |
| 22d3e70 | Luke Zappia | 30 January 2023, 10:25:12 UTC | Bump version and update NEWS | 30 January 2023, 10:25:12 UTC |
| 0c95f49 | 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. | 30 January 2023, 10:20:42 UTC |
| 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 |
