| c54e57d | David Collins | 19 March 2024, 12:18:35 UTC | Merge pull request #8638 from satijalab/develop Release/5.0.3 | 19 March 2024, 12:18:35 UTC |
| b1a8c8f | David Collins | 18 March 2024, 21:04:55 UTC | Fixup docs for LoadAkoya... again | 18 March 2024, 21:04:55 UTC |
| 2da392b | David Collins | 18 March 2024, 19:27:19 UTC | Fixup docs for LoadAkoya | 18 March 2024, 19:28:27 UTC |
| 1cf62ec | David Collins | 18 March 2024, 18:06:34 UTC | Merge pull request #8625 from satijalab/release/5.0.3 Prep for release of 5.0.3 | 18 March 2024, 18:06:34 UTC |
| 72c3cf6 | David Collins | 18 March 2024, 15:44:25 UTC | Bump date | 18 March 2024, 15:44:25 UTC |
| 9d22f91 | David Collins | 14 March 2024, 13:43:14 UTC | Update cran-comments | 14 March 2024, 20:48:15 UTC |
| bf08c98 | David Collins | 14 March 2024, 13:35:05 UTC | Update NEWS | 14 March 2024, 20:48:15 UTC |
| 1b64c51 | David Collins | 14 March 2024, 13:34:58 UTC | Update DESCRIPTION | 14 March 2024, 20:48:15 UTC |
| 964ced3 | David Collins | 14 March 2024, 20:47:25 UTC | Merge pull request #907 from satijalab/fix/misc_tests Small test fixes | 14 March 2024, 20:47:25 UTC |
| 629e110 | David Collins | 14 March 2024, 20:05:53 UTC | Bump version | 14 March 2024, 20:05:53 UTC |
| 9df0e7b | David Collins | 14 March 2024, 19:49:05 UTC | Increase tolerance for all tests in test_integration5.R | 14 March 2024, 19:49:24 UTC |
| 69d4659 | David Collins | 14 March 2024, 18:44:15 UTC | Wrap SCTransform tests in suppressWarnings | 14 March 2024, 19:34:07 UTC |
| 183f76f | David Collins | 14 March 2024, 19:33:15 UTC | Merge pull request #905 from satijalab/PercentAbove_fix Fix NA handling in PercentAbove | 14 March 2024, 19:33:15 UTC |
| 94e5718 | David Collins | 14 March 2024, 12:37:10 UTC | Update NEWS | 14 March 2024, 18:31:00 UTC |
| 092856f | David Collins | 14 March 2024, 12:35:09 UTC | Bump version | 14 March 2024, 18:31:00 UTC |
| 8c1cd28 | David Collins | 14 March 2024, 12:34:39 UTC | Cleanup PercentAbove | 14 March 2024, 18:30:59 UTC |
| 674cfb9 | David Collins | 13 March 2024, 20:49:21 UTC | Add test for PercentAbove | 14 March 2024, 18:30:34 UTC |
| a1be107 | Longda | 12 March 2024, 18:45:53 UTC | fixing NA bug in PercentAbove | 14 March 2024, 17:55:17 UTC |
| e85d963 | David Collins | 14 March 2024, 17:53:16 UTC | Merge pull request #903 from satijalab/ig_featurescatter Added option to use FeatureScatter on the log scale | 14 March 2024, 17:53:16 UTC |
| 104ad9f | David Collins | 14 March 2024, 12:31:18 UTC | Update NEWS | 14 March 2024, 12:31:18 UTC |
| c3f2a28 | David Collins | 14 March 2024, 12:30:37 UTC | Bump version | 14 March 2024, 12:30:37 UTC |
| 82873b3 | David Collins | 14 March 2024, 12:30:10 UTC | Update docs | 14 March 2024, 12:30:10 UTC |
| 369a46e | Izzy Grabski | 08 March 2024, 21:31:23 UTC | Added option to use FeatureScatter on the log scale | 14 March 2024, 12:25:42 UTC |
| 0690783 | David Collins | 13 March 2024, 20:39:17 UTC | Merge pull request #906 from satijalab/fix/sct_clip_range Fix for clip.range in SCTransform | 13 March 2024, 20:39:17 UTC |
| a077094 | David Collins | 13 March 2024, 15:05:02 UTC | Update NEWS | 13 March 2024, 15:05:02 UTC |
| 709a64a | David Collins | 13 March 2024, 15:04:56 UTC | Bump version | 13 March 2024, 15:04:56 UTC |
| 8d7bf3c | David Collins | 13 March 2024, 13:58:39 UTC | Fix clip.range handling in SCTransfrom.StdAssay | 13 March 2024, 14:42:35 UTC |
| 8ca1dbc | David Collins | 13 March 2024, 14:14:12 UTC | Add test for SCTransform's `clip.range` param | 13 March 2024, 14:42:35 UTC |
| 8b8070e | David Collins | 12 March 2024, 20:18:03 UTC | Drop duplicate test for SCTransform v2 | 13 March 2024, 14:14:53 UTC |
| 656fc8b | David Collins | 29 February 2024, 13:44:33 UTC | Merge pull request #8550 from satijalab/develop Seurat v5.0.2 | 29 February 2024, 13:44:33 UTC |
| 2b9ee19 | David Collins | 28 February 2024, 18:47:15 UTC | Merge pull request #8484 from satijalab/release/5.0.2 Prep for release of 5.0.2 | 28 February 2024, 18:47:15 UTC |
| dd4d754 | David Collins | 16 February 2024, 17:47:13 UTC | Tweak tolerances in test_integration5 Updates to pass macOS builder checks | 28 February 2024, 16:16:28 UTC |
| d489e47 | David Collins | 15 February 2024, 18:53:03 UTC | Update cran-comments | 28 February 2024, 16:16:28 UTC |
| 2ae0af2 | David Collins | 14 February 2024, 20:39:38 UTC | Update NEWS | 28 February 2024, 16:16:28 UTC |
| e9868e6 | David Collins | 12 February 2024, 16:51:32 UTC | Update DESCRIPTION Bump version | 28 February 2024, 16:16:28 UTC |
| 6a3ef5e | David Collins | 27 February 2024, 20:35:53 UTC | Merge pull request #901 from satijalab/fix/average_expression Fix `AverageExpression` to properly handle `features` param when `layer="scale.data"` and `return.seurat=TRUE` | 27 February 2024, 20:35:53 UTC |
| d0fb411 | David Collins | 27 February 2024, 20:30:45 UTC | Tweak NEWS | 27 February 2024, 20:33:42 UTC |
| 84266a2 | David Collins | 26 February 2024, 17:39:41 UTC | Bump version | 27 February 2024, 19:46:45 UTC |
| 7c54a57 | David Collins | 26 February 2024, 17:39:23 UTC | Update NEWS | 27 February 2024, 19:46:45 UTC |
| b9bd3cf | David Collins | 26 February 2024, 17:12:06 UTC | PseudobulkExpression.Seurat accepts feature vector | 27 February 2024, 19:46:45 UTC |
| df33f4d | David Collins | 26 February 2024, 17:04:14 UTC | Add test case AverageExpression bug AverageExpression( ..., layer = "scale.data", return.seurat = TRUE, features = c(...), ... ) | 27 February 2024, 19:46:45 UTC |
| 42a6583 | David Collins | 27 February 2024, 19:45:24 UTC | Merge pull request #900 from satijalab/fix/pseudobulk_fc Add fc.slot parameter to FindMarkers | 27 February 2024, 19:45:24 UTC |
| 21a9b3c | David Collins | 27 February 2024, 13:40:18 UTC | Update docs | 27 February 2024, 13:40:18 UTC |
| 239e24f | David Collins | 27 February 2024, 13:27:01 UTC | Override descriptions for logfc.threshold param in mixscape.R | 27 February 2024, 13:39:31 UTC |
| 33038d7 | David Collins | 26 February 2024, 20:06:10 UTC | Tweak docstring for fc.slot | 27 February 2024, 13:39:31 UTC |
| 9de3175 | David Collins | 23 February 2024, 22:35:09 UTC | Swap `scaled` param back out for `slot` in FindMarkers.default | 27 February 2024, 13:39:31 UTC |
| 0253131 | David Collins | 22 February 2024, 21:52:58 UTC | Update test_differential_expression.R Set fc.slot="counts" to reflect previous behavior | 27 February 2024, 13:39:31 UTC |
| b1b59b5 | David Collins | 22 February 2024, 21:47:09 UTC | Add `fc.slot` param to FindMarkers | 27 February 2024, 13:39:31 UTC |
| ed72030 | David Collins | 22 February 2024, 21:09:14 UTC | Cleanup FindMarkers Replace `slot` param with `scaled` param in FindMarkers.default Drop unused params Drop redundant params Re-organize docstrings Use double instead of single quotes | 27 February 2024, 13:39:31 UTC |
| f9e92c9 | David Collins | 22 February 2024, 22:04:16 UTC | Bump version | 27 February 2024, 13:39:31 UTC |
| 8504229 | David Collins | 22 February 2024, 22:03:54 UTC | Update NEWS | 27 February 2024, 13:39:31 UTC |
| 942766a | David Collins | 14 February 2024, 20:38:50 UTC | Merge pull request #898 from satijalab/fix/test_integration Improve tests for IntegrateLayers | 14 February 2024, 20:38:50 UTC |
| 120265e | David Collins | 07 February 2024, 18:59:22 UTC | Bump version | 14 February 2024, 18:14:55 UTC |
| b025ea0 | David Collins | 06 February 2024, 18:11:02 UTC | Add test_integration5.R Implement new tests for IntegrateLayers Better checks in tests for IntegrateLayers Even better checks in tests for IntegrateLayers Tests for IntegrateLayers use SCTransform v1 Fix flakiness in test_integration5.R Fix flakiness in test_integration5.R (for real this time) | 14 February 2024, 18:14:55 UTC |
| 1c629e4 | David Collins | 06 February 2024, 18:10:38 UTC | Drop tests for IntegrateLayers from test_integratedata.R | 07 February 2024, 19:39:36 UTC |
| 150a85b | David Collins | 07 February 2024, 19:39:17 UTC | Merge pull request #897 from satijalab/fix/test_dimensional_reduction Skip testing PCA with BPCells if the latter is not installed | 07 February 2024, 19:39:17 UTC |
| e40f409 | David Collins | 07 February 2024, 18:58:43 UTC | Bump version | 07 February 2024, 18:58:43 UTC |
| e68cc87 | David Collins | 18 January 2024, 18:18:09 UTC | Skip test if BPCells not installed | 07 February 2024, 14:11:56 UTC |
| fc3bbe2 | David Collins | 07 February 2024, 14:09:49 UTC | Merge pull request #896 from satijalab/fix/sctransform_fixes Fixes for SCTransform using `vars.to.regress` | 07 February 2024, 14:09:49 UTC |
| 5d3fdc5 | David Collins | 06 February 2024, 19:47:24 UTC | Suppress warnings from SCTransform during testing | 06 February 2024, 19:47:24 UTC |
| 2d393d1 | David Collins | 05 February 2024, 17:04:33 UTC | Add test for `SCTransform` using `vars.to.regress` | 06 February 2024, 16:39:34 UTC |
| ccaa1e8 | Saket Choudhary | 05 February 2024, 22:52:13 UTC | scale data when fetching residuals for union of features | 05 February 2024, 23:01:23 UTC |
| e7c5873 | Saket Choudhary | 30 January 2024, 14:47:41 UTC | Style fixes | 05 February 2024, 23:01:23 UTC |
| e8671a9 | Saket Choudhary | 26 January 2024, 23:17:46 UTC | Update NEWS; bump version | 05 February 2024, 16:54:31 UTC |
| 6cc1103 | Saket Choudhary | 26 January 2024, 23:17:32 UTC | Documentation | 05 February 2024, 16:53:29 UTC |
| 0b9742b | Saket Choudhary | 26 January 2024, 23:13:30 UTC | Fix SCTransform to allow regressing features in StdAssay | 05 February 2024, 16:53:29 UTC |
| 4404e21 | Saket Choudhary | 26 January 2024, 21:04:38 UTC | SCTransform: prevent double feature checking when setting variable features on multiple assays | 05 February 2024, 16:53:29 UTC |
| 9ad1627 | David Collins | 29 January 2024, 17:59:13 UTC | Merge branch 'fix/scVIIntegration' into develop | 29 January 2024, 17:59:13 UTC |
| bc14764 | David Collins | 22 January 2024, 21:37:25 UTC | Revert NEWS | 25 January 2024, 16:47:50 UTC |
| 3e2bfc1 | David Collins | 22 January 2024, 15:18:41 UTC | Bump version | 25 January 2024, 16:47:49 UTC |
| 2935c2e | David Collins | 22 January 2024, 21:34:57 UTC | Revert "Fix scVIIntegration to correctly populate feature and cell metadata" This reverts commit ebc65473b8cb5567e347f77951f1bc3626f9b3ac. | 22 January 2024, 21:34:57 UTC |
| 938698c | Saket Choudhary | 19 January 2024, 21:35:02 UTC | Merge pull request #894 from satijalab/fix/scvi_integration Fix/scvi integration | 19 January 2024, 21:35:02 UTC |
| bf9764e | Saket Choudhary | 19 January 2024, 18:56:01 UTC | Bump news; update version | 19 January 2024, 18:56:01 UTC |
| ebc6547 | Saket Choudhary | 19 January 2024, 18:55:41 UTC | Fix scVIIntegration to correctly populate feature and cell metadata | 19 January 2024, 18:55:41 UTC |
| 1dfe644 | gesmira | 12 January 2024, 21:54:06 UTC | Merge pull request #892 from satijalab/fix/rpca_bp Fixes RPCAIntegration bug related to BPCells | 12 January 2024, 21:54:06 UTC |
| c76a70e | Gesmira | 11 January 2024, 15:04:16 UTC | format | 11 January 2024, 15:04:16 UTC |
| f38ecc3 | Gesmira | 09 January 2024, 22:11:04 UTC | bump version | 10 January 2024, 15:07:36 UTC |
| 00883a1 | Gesmira | 09 January 2024, 21:53:44 UTC | set only data layer in new objects | 10 January 2024, 15:07:36 UTC |
| 00a9d2a | Saket Choudhary | 19 December 2023, 05:52:54 UTC | Merge pull request #889 from satijalab/fix/sct Fix SCTransform to handle residuals for single features and honor vars.to.regress | 19 December 2023, 05:52:54 UTC |
| af035e5 | Saket Choudhary | 19 December 2023, 05:51:50 UTC | Bump version; update NEWS | 19 December 2023, 05:51:50 UTC |
| 43d673c | Saket Choudhary | 19 December 2023, 05:50:20 UTC | Bump version; update NEWS | 19 December 2023, 05:50:20 UTC |
| 64a6495 | Saket Choudhary | 19 December 2023, 05:50:01 UTC | Fix SCTransform to handle residuals for single features and honor vars.to.regress | 19 December 2023, 05:50:01 UTC |
| 41d19a8 | Gesmira | 20 November 2023, 15:50:22 UTC | Merge remote-tracking branch 'private/release/5.0.1' | 20 November 2023, 15:50:22 UTC |
| f3fbb2b | Gesmira | 16 November 2023, 19:57:23 UTC | bump version | 16 November 2023, 19:57:23 UTC |
| ab25439 | Gesmira | 16 November 2023, 19:56:26 UTC | update NEWS | 16 November 2023, 19:56:26 UTC |
| b0671a3 | Zhuoyan Li | 16 November 2023, 18:20:34 UTC | Merge pull request #878 from satijalab/lis_vignette_updates Updates for vignette and website config files | 16 November 2023, 18:20:34 UTC |
| 51752a5 | zskylarli | 16 November 2023, 17:15:32 UTC | Merge branch 'lis_vignette_updates' of https://github.com/satijalab/seurat-private into lis_vignette_updates | 16 November 2023, 17:15:32 UTC |
| ee17666 | zskylarli | 16 November 2023, 17:14:37 UTC | fix typo | 16 November 2023, 17:14:37 UTC |
| 41c2c5e | mhkowalski | 16 November 2023, 16:55:58 UTC | update de_vignette.Rmd with new AggregateExpression meta.data | 16 November 2023, 16:55:58 UTC |
| 683a11f | zskylarli | 16 November 2023, 16:47:11 UTC | Merge branch 'develop' of https://github.com/satijalab/seurat-private into lis_vignette_updates | 16 November 2023, 16:47:11 UTC |
| 8494d3b | zskylarli | 16 November 2023, 16:45:14 UTC | changed parsebio vig for AggregateExp updates | 16 November 2023, 16:45:14 UTC |
| 8db2d94 | zskylarli | 15 November 2023, 22:11:49 UTC | added covid vignette | 15 November 2023, 22:11:49 UTC |
| 6b62200 | gesmira | 15 November 2023, 21:58:03 UTC | Merge pull request #877 from satijalab/lis_runazimuth_debug Fix mapping score bug with duplicate cell names | 15 November 2023, 21:58:03 UTC |
| 44e06b5 | zskylarli | 13 November 2023, 23:17:46 UTC | bump version | 15 November 2023, 21:55:06 UTC |
| 891cd23 | zskylarli | 13 November 2023, 23:15:39 UTC | fix for issue #7922 | 15 November 2023, 21:55:06 UTC |
| f828377 | mhkowalski | 15 November 2023, 21:54:49 UTC | Merge pull request #880 from satijalab/fix/fetch_data_nas Update visualization functions if NAs in meta-data | 15 November 2023, 21:54:49 UTC |
| b21132e | mhkowalski | 15 November 2023, 21:51:20 UTC | bump version | 15 November 2023, 21:51:20 UTC |
| 1e70485 | Gesmira | 15 November 2023, 15:05:07 UTC | same fix for FeatureScatter | 15 November 2023, 21:49:08 UTC |
| 75ac019 | mhkowalski | 14 November 2023, 18:28:51 UTC | update dimplot to handle NAs in split.by variable | 15 November 2023, 21:49:08 UTC |
| 59e861d | Gesmira | 15 November 2023, 21:38:46 UTC | resolve conflict | 15 November 2023, 21:38:46 UTC |
