| 245d72b | satijalab | 16 June 2019, 18:37:31 UTC | Merge pull request #1692 from satijalab/develop Seurat v3.0.2 | 16 June 2019, 18:37:31 UTC |
| 1198f32 | Paul Hoffman | 14 June 2019, 20:33:28 UTC | Merge pull request #126 from satijalab/fix/UpdateDocs Update docs for CRAN submission | 14 June 2019, 20:33:28 UTC |
| a8b3ab9 | Paul Hoffman | 14 June 2019, 20:32:17 UTC | Update date | 14 June 2019, 20:32:17 UTC |
| ffb1884 | Paul Hoffman | 14 June 2019, 19:40:52 UTC | Address satijalab/seurat#1634 Fix issue where we were calling levels on a vector | 14 June 2019, 19:40:52 UTC |
| 68b4335 | Paul Hoffman | 14 June 2019, 16:15:17 UTC | Fix to blended FeaturePlot | 14 June 2019, 16:15:17 UTC |
| 91f4952 | Paul Hoffman | 12 June 2019, 20:47:13 UTC | Update NEWS | 12 June 2019, 20:47:13 UTC |
| 312c10b | Paul Hoffman | 12 June 2019, 20:43:30 UTC | Merge branch 'develop' into fix/UpdateDocs | 12 June 2019, 20:43:30 UTC |
| 93d2425 | Andrew Butler | 12 June 2019, 20:42:38 UTC | Merge pull request #131 from satijalab/fix/DevelopMergeConflict Fix merge conflicts | 12 June 2019, 20:42:38 UTC |
| e301651 | Paul Hoffman | 12 June 2019, 20:39:41 UTC | Fix merge conflicts | 12 June 2019, 20:39:41 UTC |
| b353c87 | Andrew Butler | 12 June 2019, 20:36:49 UTC | Merge pull request #122 from satijalab/feat/SCT_ncells downsampling cells for NB regression | 12 June 2019, 20:36:49 UTC |
| fae8ec1 | Andrew Butler | 12 June 2019, 20:35:36 UTC | bump develop version | 12 June 2019, 20:35:36 UTC |
| a29bb74 | Paul Hoffman | 12 June 2019, 20:35:05 UTC | Merge branch 'develop' into fix/UpdateDocs | 12 June 2019, 20:35:05 UTC |
| 5723f6a | Andrew Butler | 12 June 2019, 20:34:32 UTC | Merge branch 'develop' into feat/SCT_ncells | 12 June 2019, 20:34:32 UTC |
| 90e9ca8 | Andrew Butler | 12 June 2019, 20:33:09 UTC | add some basic tests for SCTransform wrapper function | 12 June 2019, 20:33:09 UTC |
| 5ffa7ae | Andrew Butler | 11 June 2019, 19:32:55 UTC | Merge pull request #130 from satijalab/feat/ListSeuratCommand New as.list method for SeuratCommand objects | 11 June 2019, 19:32:55 UTC |
| e958e16 | Andrew Butler | 11 June 2019, 19:31:35 UTC | bump develop version | 11 June 2019, 19:31:35 UTC |
| b182af8 | Andrew Butler | 11 June 2019, 19:31:02 UTC | Merge branch 'develop' into feat/ListSeuratCommand | 11 June 2019, 19:31:02 UTC |
| a798918 | Andrew Butler | 11 June 2019, 19:25:05 UTC | Merge pull request #129 from satijalab/feat/DefaultDimReduc New function to find the default dimensional reduction | 11 June 2019, 19:25:05 UTC |
| 57cb9d3 | Andrew Butler | 11 June 2019, 19:24:04 UTC | bump develop version | 11 June 2019, 19:24:04 UTC |
| ab01b13 | Paul Hoffman | 11 June 2019, 17:28:18 UTC | New as.list method for SeuratCommand objects Coerces SeuratCommand objects to lists for easy extraction of parameters | 11 June 2019, 17:28:18 UTC |
| 4c3956e | Paul Hoffman | 10 June 2019, 23:04:27 UTC | devtools::document updated this | 10 June 2019, 23:04:27 UTC |
| aa979e3 | Paul Hoffman | 10 June 2019, 23:02:08 UTC | New function to find the default dimensional reduction Finds a DimReduc matching umap, tnse, or pca, in that order Prioritises DimReducs with the same default assay as the object or assay specified | 10 June 2019, 23:02:08 UTC |
| eb539b5 | Paul Hoffman | 10 June 2019, 20:54:50 UTC | Merge pull request #128 from satijalab/fix/HighlightColors Better default highlighting colors | 10 June 2019, 20:54:50 UTC |
| 9393ed4 | Paul Hoffman | 10 June 2019, 20:54:25 UTC | Bump develop version | 10 June 2019, 20:54:25 UTC |
| 1983f30 | Andrew Butler | 10 June 2019, 20:44:40 UTC | update colors in CellSelector as well | 10 June 2019, 20:44:40 UTC |
| 6d292e1 | Andrew Butler | 10 June 2019, 20:33:54 UTC | better defaults for highlighting colors | 10 June 2019, 20:33:54 UTC |
| c530568 | Paul Hoffman | 10 June 2019, 20:00:21 UTC | Merge pull request #127 from satijalab/fix/SCEIdents set the active.idents when converting from SCE (#1566) | 10 June 2019, 20:00:21 UTC |
| eb566c9 | Paul Hoffman | 10 June 2019, 20:00:07 UTC | Bump develop version | 10 June 2019, 20:00:07 UTC |
| 25dbfed | Andrew Butler | 10 June 2019, 13:27:35 UTC | set the active.idents when converting from SCE (#1566) | 10 June 2019, 13:27:35 UTC |
| dcd58c5 | Paul Hoffman | 05 June 2019, 20:36:12 UTC | Update docs for CRAN submission | 05 June 2019, 20:36:12 UTC |
| de86368 | Andrew Butler | 05 June 2019, 17:22:18 UTC | Merge pull request #125 from satijalab/fix/SplitScaleData Provide a fix for split `ScaleData` | 05 June 2019, 17:22:18 UTC |
| aa401bb | Andrew Butler | 05 June 2019, 17:21:06 UTC | bump develop version | 05 June 2019, 17:21:06 UTC |
| a6ec432 | Paul Hoffman | 05 June 2019, 16:45:54 UTC | devtools::document updated these | 05 June 2019, 16:45:54 UTC |
| b071285 | Paul Hoffman | 05 June 2019, 16:41:00 UTC | Provide a fix for split scaledata There was an issue using future_apply for the split It would return a matrix with the number of columns equal to the number of blocks Reshaping using dim didn't fix it Switched to future_lapply to force a list of matrices to be returned | 05 June 2019, 16:41:00 UTC |
| 6653884 | Andrew Butler | 05 June 2019, 13:33:57 UTC | Merge pull request #124 from satijalab/fix/findneighbors Fix bug in FindNeighbors when using distance matrix | 05 June 2019, 13:33:57 UTC |
| 9e9e5cf | Andrew Butler | 05 June 2019, 13:31:44 UTC | bump develop version | 05 June 2019, 13:31:44 UTC |
| f2d0dfc | Paul Hoffman | 04 June 2019, 21:41:31 UTC | Merge branch 'develop' into feat/SCT_ncells | 04 June 2019, 21:41:31 UTC |
| 007d9ce | Paul Hoffman | 04 June 2019, 21:40:15 UTC | devtools::document updated these | 04 June 2019, 21:40:15 UTC |
| d35908d | Paul Hoffman | 04 June 2019, 21:39:07 UTC | Adjust style | 04 June 2019, 21:39:07 UTC |
| 541e8df | timoast | 04 June 2019, 21:19:27 UTC | Fix bug when using distance matrix when some cells were no other cells neighbors | 04 June 2019, 21:19:27 UTC |
| 8f69ca2 | Paul Hoffman | 04 June 2019, 18:02:03 UTC | Merge pull request #121 from satijalab/fix/FeaturePlotMinMax fix min/max cutoff values for FeaturePlot | 04 June 2019, 18:02:03 UTC |
| c114db2 | Paul Hoffman | 04 June 2019, 18:00:45 UTC | Bump develop version | 04 June 2019, 18:00:45 UTC |
| 081dbf1 | Paul Hoffman | 04 June 2019, 17:58:02 UTC | Merge branch 'develop' into fix/FeaturePlotMinMax | 04 June 2019, 17:58:02 UTC |
| f388321 | Andrew Butler | 04 June 2019, 17:44:34 UTC | bump develop version | 04 June 2019, 17:44:34 UTC |
| 0379fa9 | Andrew Butler | 04 June 2019, 17:43:06 UTC | Merge pull request #123 from satijalab/fix/DoHeatmapOrdering preserve factor levels appropriately (#1632) | 04 June 2019, 17:43:06 UTC |
| 18ecc4b | Andrew Butler | 04 June 2019, 17:37:19 UTC | preserve factor levels appropriately (#1632) | 04 June 2019, 17:37:19 UTC |
| 34e75b7 | Andrew Butler | 04 June 2019, 15:48:14 UTC | Merge branch 'develop' of github.com:satijalab/seurat into develop | 04 June 2019, 15:48:14 UTC |
| d7d87a2 | Andrew Butler | 04 June 2019, 15:41:41 UTC | Merge pull request #1627 from alexvpickering/alexvpickering-patch-2 exclude assays without data in as.SingleCellExperiment | 04 June 2019, 15:41:41 UTC |
| 5d713cd | Andrew Butler | 04 June 2019, 15:41:14 UTC | bump develop version | 04 June 2019, 15:41:14 UTC |
| d18837b | Andrew Butler | 04 June 2019, 15:13:11 UTC | minor style tweak | 04 June 2019, 15:13:11 UTC |
| 2931fe6 | Alex Pickering | 04 June 2019, 02:05:57 UTC | exclude assays without data in as.SingleCellExperiment This commit fixes #1626 | 04 June 2019, 02:05:57 UTC |
| 9eb8821 | yuhanH | 03 June 2019, 18:34:30 UTC | downsampleing cells for NB regression | 03 June 2019, 18:34:30 UTC |
| d88b379 | Andrew Butler | 03 June 2019, 17:51:51 UTC | fix min/max cutoff values for FeaturePlot | 03 June 2019, 17:51:51 UTC |
| a0d9d26 | Andrew Butler | 31 May 2019, 18:29:00 UTC | Merge pull request #120 from satijalab/fix/ROCDocs fix return value in ROC DE test docs | 31 May 2019, 18:29:00 UTC |
| cfedb57 | Andrew Butler | 31 May 2019, 14:34:43 UTC | fix return value in ROC DE test docs | 31 May 2019, 14:34:43 UTC |
| 3644041 | Andrew Butler | 30 May 2019, 17:37:52 UTC | Merge pull request #1605 from chenyenchung/develop Let TransferData() handle a matrix in refdata | 30 May 2019, 17:37:52 UTC |
| fc9ad3a | Andrew Butler | 30 May 2019, 17:09:47 UTC | bump develop version | 30 May 2019, 17:09:47 UTC |
| 73eb4ab | Andrew Butler | 30 May 2019, 17:09:19 UTC | Merge branch 'develop' of github.com:satijalab/seurat into develop | 30 May 2019, 17:09:19 UTC |
| f63bca3 | Andrew Butler | 30 May 2019, 17:08:03 UTC | Merge pull request #117 from satijalab/feat/GetResidual_error_develop GetResidual branch off develop | 30 May 2019, 17:08:03 UTC |
| 8e29664 | Andrew Butler | 30 May 2019, 17:02:26 UTC | ensure sparse matrix is a dgCMatrix before creating the new assay | 30 May 2019, 17:02:26 UTC |
| 62fb26c | Andrew Butler | 30 May 2019, 15:31:35 UTC | bump develop version | 30 May 2019, 15:31:35 UTC |
| d379203 | Andrew Butler | 30 May 2019, 15:31:12 UTC | Merge branch 'develop' into feat/GetResidual_error_develop | 30 May 2019, 15:31:12 UTC |
| ba8abca | Andrew Butler | 30 May 2019, 15:29:54 UTC | only need one return statement | 30 May 2019, 15:29:54 UTC |
| b124961 | Andrew Butler | 30 May 2019, 15:26:31 UTC | small changes to warning, message respects verbose | 30 May 2019, 15:26:31 UTC |
| 10aff00 | Andrew Butler | 30 May 2019, 15:20:33 UTC | style tweaks | 30 May 2019, 15:20:33 UTC |
| 46bc921 | Andrew Butler | 30 May 2019, 15:11:43 UTC | Merge branch 'develop' of github.com:satijalab/seurat into develop | 30 May 2019, 15:11:43 UTC |
| d9452af | Andrew Butler | 30 May 2019, 15:03:08 UTC | Merge pull request #1603 from HenrikBengtsson/develop BUG FIX: Seurat:::PlanThreads() assumes the 'future' attached | 30 May 2019, 15:03:08 UTC |
| d68b645 | yuhanH | 30 May 2019, 14:35:14 UTC | branch off develop | 30 May 2019, 14:35:14 UTC |
| 037e14a | Andrew Butler | 30 May 2019, 13:40:28 UTC | replace PlanThreads with nbrOfWorkers | 30 May 2019, 13:40:28 UTC |
| fa0b01e | Yen-Chung Chen | 30 May 2019, 05:04:12 UTC | Merge pull request #1 from chenyenchung/Patch_TransferData Make sure refdata in TransferData() is sparse | 30 May 2019, 05:04:12 UTC |
| 414b022 | Yen-Chung Chen | 29 May 2019, 21:36:46 UTC | Make sure refdata in TransferData() is sparse To make sure the later [matrix multiplication](https://github.com/chenyenchung/seurat/blob/f195c4a75081713d057e648430a4d288ca752835/R/integration.R#L1033) gives a `dgCMatrix`, `refdata.anchors` must be a `dgCMatrix` but not a `matrix`. Otherwise, `new.data` will be a `dgematrix` and will not be compatible with `[CreateAssayObject(counts = new.data)](https://github.com/chenyenchung/seurat/blob/f195c4a75081713d057e648430a4d288ca752835/R/integration.R#L1037)`. | 29 May 2019, 21:36:46 UTC |
| fa086a3 | Andrew Butler | 29 May 2019, 20:44:04 UTC | Merge pull request #115 from satijalab/fix/SCTFindAllMarkers Fixed FindAllMarkers to work with SCT data | 29 May 2019, 20:44:04 UTC |
| 71a57ba | Andrew Butler | 29 May 2019, 20:41:13 UTC | minor style tweak | 29 May 2019, 20:41:13 UTC |
| 10a1db5 | Andrew Butler | 29 May 2019, 20:16:23 UTC | Merge pull request #114 from satijalab/fix/ClusteringLevels Fixes to clustering levels | 29 May 2019, 20:16:23 UTC |
| ec270e9 | papal22e | 29 May 2019, 20:09:52 UTC | fix FindAllMarkers for SCTransform | 29 May 2019, 20:09:52 UTC |
| b496685 | Henrik Bengtsson | 29 May 2019, 19:29:19 UTC | Hmmm... what's up with that noise automatically added when you run roxygen?!? | 29 May 2019, 19:29:30 UTC |
| 063c9d7 | Henrik Bengtsson | 29 May 2019, 19:16:50 UTC | BUG FIX: Seurat:::PlanThreads() assumes the 'future' package is attached - minimal fix [#1602] | 29 May 2019, 19:16:50 UTC |
| 7d92675 | Paul Hoffman | 29 May 2019, 19:10:24 UTC | Fixes to clustering levels FindClusters.Seurat now properly sorts by numeric value levels<-.Seurat now reorders levels rather than changing the factor groups | 29 May 2019, 19:10:24 UTC |
| c90c146 | Efi Papalexi | 28 May 2019, 16:38:06 UTC | Merge pull request #112 from satijalab/fix/PosDEFilter fix only.pos fitlering | 28 May 2019, 16:38:06 UTC |
| e364cce | Andrew Butler | 28 May 2019, 16:21:47 UTC | fix only.pos fitlering | 28 May 2019, 16:21:47 UTC |
| fff6898 | Andrew Butler | 24 May 2019, 16:42:36 UTC | bump develop version | 24 May 2019, 16:42:36 UTC |
| d8a2dd5 | Paul Hoffman | 24 May 2019, 16:26:43 UTC | Merge pull request #108 from satijalab/fix/SCT_BuildClusterTree add use.scale/counts params to BuildClusterTree | 24 May 2019, 16:26:43 UTC |
| 9f79a85 | Paul Hoffman | 24 May 2019, 16:25:53 UTC | Merge pull request #106 from satijalab/fix/mergeMetadata fix metadata merging with duplicated cellnames | 24 May 2019, 16:25:53 UTC |
| 90d5332 | Paul Hoffman | 24 May 2019, 16:23:42 UTC | Merge branch 'develop' into fix/mergeMetadata | 24 May 2019, 16:23:42 UTC |
| e6f5f50 | Paul Hoffman | 24 May 2019, 16:23:16 UTC | Merge branch 'develop' of github.com:satijalab/seurat-private into develop | 24 May 2019, 16:23:16 UTC |
| f6e05fe | Andrew Butler | 24 May 2019, 16:22:15 UTC | Merge pull request #107 from satijalab/fix/IdentFactorLevels ensure factor levels are numerically increasing after FindClusters | 24 May 2019, 16:22:15 UTC |
| bb2ceca | Paul Hoffman | 24 May 2019, 16:22:10 UTC | Update documentation | 24 May 2019, 16:22:10 UTC |
| 09bd054 | Tim Stuart | 24 May 2019, 16:20:27 UTC | Merge pull request #110 from satijalab/fix/FeaturePlotDoc Fix description of object returned by FeaturePlot | 24 May 2019, 16:20:27 UTC |
| ec374bb | Tim Stuart | 24 May 2019, 16:18:19 UTC | Merge pull request #109 from satijalab/fix/UpdateKey Add check for missing dimreduc key; closes #1553 | 24 May 2019, 16:18:19 UTC |
| b5f2b43 | timoast | 24 May 2019, 16:08:02 UTC | Fix description of object returned by FeaturePlot | 24 May 2019, 16:08:02 UTC |
| e2d567c | Andrew Butler | 24 May 2019, 16:06:28 UTC | remove commented out code | 24 May 2019, 16:06:28 UTC |
| da7bc6d | Andrew Butler | 24 May 2019, 15:54:05 UTC | safer regex, if no columnnames use name of dr | 24 May 2019, 15:54:05 UTC |
| b6a1cc3 | timoast | 24 May 2019, 15:20:01 UTC | Add check for missing dimreduc key; closes #1553 | 24 May 2019, 15:20:01 UTC |
| c0a126b | Paul Hoffman | 24 May 2019, 15:17:25 UTC | Replace use.counts and use.scale with slot | 24 May 2019, 15:17:25 UTC |
| 3614d6f | Paul Hoffman | 24 May 2019, 15:15:14 UTC | devtools::document updated this | 24 May 2019, 15:15:14 UTC |
| b0aadc2 | Paul Hoffman | 24 May 2019, 15:13:55 UTC | Changes to AverageExpression Add new slot parameter Deprecate use.counts and use.scale | 24 May 2019, 15:13:55 UTC |
| 9bd8cb8 | Andrew Butler | 24 May 2019, 13:23:19 UTC | add use.scale/counts params to BuildClusterTree | 24 May 2019, 13:23:19 UTC |
| 1bc779c | Andrew Butler | 24 May 2019, 13:09:51 UTC | ensure factor levels are numerically increasing after FindClusters (#1529) | 24 May 2019, 13:10:22 UTC |
| 9f9914f | Andrew Butler | 23 May 2019, 20:34:13 UTC | use existing internal function | 23 May 2019, 20:45:41 UTC |
| e0a7779 | Andrew Butler | 23 May 2019, 19:48:33 UTC | fix metadata merging with duplicated cellnames | 23 May 2019, 19:48:33 UTC |
