| 25b830b | satijalab | 16 April 2019, 13:15:44 UTC | Merge pull request #1375 from satijalab/release/3.0 Seurat v3 | 16 April 2019, 13:15:44 UTC |
| 103f6f6 | Paul Hoffman | 15 April 2019, 22:31:57 UTC | Update README.md | 15 April 2019, 22:31:57 UTC |
| 209717b | Paul Hoffman | 15 April 2019, 20:17:35 UTC | Update pbmc_small to latest v3 standards | 15 April 2019, 20:17:35 UTC |
| f96309a | Paul Hoffman | 15 April 2019, 20:16:07 UTC | Fix for UpdateSeuratObject Don't run the v2 routine for v3 objects | 15 April 2019, 20:16:07 UTC |
| 0f4e519 | Paul Hoffman | 15 April 2019, 18:22:06 UTC | Merge pull request #49 from satijalab/fix/DocUpdates update NEWS and README, version bump for CRAN | 15 April 2019, 18:22:06 UTC |
| b818351 | Paul Hoffman | 15 April 2019, 18:21:36 UTC | Merge branch 'release/3.0' into fix/DocUpdates | 15 April 2019, 18:21:36 UTC |
| d791dc1 | Paul Hoffman | 15 April 2019, 18:20:06 UTC | Merge pull request #51 from satijalab/fix/Suggest-loomR Add loomR back to suggested packages | 15 April 2019, 18:20:06 UTC |
| 6b23fb9 | Paul Hoffman | 15 April 2019, 18:11:37 UTC | Update cran-comments.md | 15 April 2019, 18:11:37 UTC |
| 5af960b | Andrew Butler | 15 April 2019, 14:05:03 UTC | add more stuff to NEWS file | 15 April 2019, 14:05:03 UTC |
| 81fc990 | Andrew Butler | 15 April 2019, 13:37:10 UTC | small doc fix for ReorderIdent example | 15 April 2019, 13:37:10 UTC |
| 788ca37 | Andrew Butler | 15 April 2019, 13:34:07 UTC | resolve merge conflict | 15 April 2019, 13:34:07 UTC |
| fdeaa1d | Paul Hoffman | 15 April 2019, 03:27:54 UTC | Add loomR as a suggested package again | 15 April 2019, 03:27:54 UTC |
| 52b7535 | Paul Hoffman | 15 April 2019, 02:57:57 UTC | Merge pull request #47 from satijalab/fix/importSCTransform Move sctransform from suggests to imports | 15 April 2019, 02:57:57 UTC |
| 6c04b1f | Paul Hoffman | 15 April 2019, 02:57:05 UTC | Merge pull request #50 from satijalab/fix/PassRDevel ensure checks pass on R devel | 15 April 2019, 02:57:05 UTC |
| 232aacf | andrewwbutler | 13 April 2019, 18:19:59 UTC | ensure checks pass on R devel | 13 April 2019, 18:19:59 UTC |
| f4a2fe8 | Andrew Butler | 12 April 2019, 23:36:13 UTC | update NEWS and README, version bump for CRAN | 12 April 2019, 23:36:13 UTC |
| ab553e6 | Andrew Butler | 12 April 2019, 18:10:13 UTC | add return value and example to SCTransform | 12 April 2019, 18:10:13 UTC |
| 6e7dc04 | Paul Hoffman | 12 April 2019, 17:37:35 UTC | Move sctransform from suggests to imports | 12 April 2019, 17:37:35 UTC |
| cc45b31 | Paul Hoffman | 12 April 2019, 14:50:15 UTC | Merge pull request #45 from satijalab/fix/FixedAssay [WIP] Keep data dimensions static in Assay objects | 12 April 2019, 14:50:15 UTC |
| 00e888c | Paul Hoffman | 12 April 2019, 14:49:58 UTC | Merge pull request #46 from satijalab/fix/NoFindMatches Remove use of utils:::findMatches so we aren't using the triple-colon | 12 April 2019, 14:49:58 UTC |
| df87dd6 | Paul Hoffman | 11 April 2019, 19:10:42 UTC | Remove use of utils:::findMatches so we aren't using the triple-colon | 11 April 2019, 19:10:42 UTC |
| 13eba93 | Paul Hoffman | 11 April 2019, 16:41:55 UTC | devtools::document updated this | 11 April 2019, 16:41:55 UTC |
| 15823a5 | Paul Hoffman | 11 April 2019, 16:39:35 UTC | Fixes to SCTransform for new Assay requierments | 11 April 2019, 16:41:39 UTC |
| a19ca58 | Paul Hoffman | 11 April 2019, 16:38:38 UTC | Add new Misc.Assay and Misc<-.Assay methods | 11 April 2019, 16:38:38 UTC |
| 16526d8 | Paul Hoffman | 11 April 2019, 16:19:55 UTC | Merge branch 'release/3.0' into fix/FixedAssay | 11 April 2019, 16:19:55 UTC |
| c10d52e | timoast | 11 April 2019, 15:45:08 UTC | update progress messages | 11 April 2019, 15:45:08 UTC |
| 17df20f | Paul Hoffman | 11 April 2019, 15:10:35 UTC | Update README.md | 11 April 2019, 15:10:35 UTC |
| 14e410d | Paul Hoffman | 11 April 2019, 14:55:53 UTC | Fix issue with static data dimensions in IntegrateData | 11 April 2019, 14:57:25 UTC |
| 9bb9a97 | Paul Hoffman | 10 April 2019, 22:42:49 UTC | Fixes to the Assay object Require that setting the data slot matches the current dimensionality of the assay object Allows adding metadata for certain features, not all | 10 April 2019, 22:42:49 UTC |
| d419e71 | Christoph Hafemeister | 10 April 2019, 21:52:52 UTC | Temp fix for setting of feature meta data in SCTransform
remove the @meta.features once automatic NA padding is part of [[<- for assay objects | 10 April 2019, 21:52:52 UTC |
| c4f69d6 | Andrew Butler | 10 April 2019, 18:56:52 UTC | Merge pull request #43 from satijalab/feature/PassDotsPlots Allow passing the dots from VlnPlot/RidgePlot to CombinePlots | 10 April 2019, 18:56:52 UTC |
| e6b6433 | Paul Hoffman | 10 April 2019, 18:54:44 UTC | Remove use of inheritDotParams Sorry Andrew | 10 April 2019, 18:54:44 UTC |
| 47df6b4 | Paul Hoffman | 10 April 2019, 18:39:58 UTC | Allow passing the dots from VlnPlot/RidgePlot to CombinePlots | 10 April 2019, 18:39:58 UTC |
| d9bffe5 | Paul Hoffman | 10 April 2019, 17:55:07 UTC | Merge pull request #42 from satijalab/integration-bugfix Fix error when using projected loadings | 10 April 2019, 17:55:07 UTC |
| ad5a94f | timoast | 10 April 2019, 17:27:16 UTC | Fix error when using projected loadings | 10 April 2019, 17:27:16 UTC |
| 1a36031 | Andrew Butler | 10 April 2019, 16:59:36 UTC | Merge pull request #41 from satijalab/fix/UpdateSeuratObject Fix/update seurat object | 10 April 2019, 16:59:36 UTC |
| 84e1d58 | Paul Hoffman | 10 April 2019, 15:56:52 UTC | Merge branch 'release/3.0' of github.com:satijalab/seurat-private into release/3.0 | 10 April 2019, 15:56:52 UTC |
| 588876f | Paul Hoffman | 10 April 2019, 15:50:13 UTC | devtools::document updated these | 10 April 2019, 15:50:13 UTC |
| 7c1c72f | Paul Hoffman | 10 April 2019, 15:48:57 UTC | Address satijalab/seurat#951 Fix issue with UpdateSeuratObject where v2 objects wouldn't go through v3 validation | 10 April 2019, 15:48:57 UTC |
| a28a548 | Paul Hoffman | 10 April 2019, 15:42:23 UTC | Merge pull request #40 from satijalab/fix/CalcN Only compute store CalcN results when counts exist (#1330) | 10 April 2019, 15:42:23 UTC |
| 5439ea9 | Andrew Butler | 10 April 2019, 15:28:43 UTC | Only compute store CalcN results when counts exist (#1330) When a new assay was added (or subset was called) on an object with nothing in the counts slot, CalcN would fill the metadata with a column of NAs. Now, CalcN will return NULL and these columns shouldn't get created. | 10 April 2019, 15:28:43 UTC |
| b563262 | Paul Hoffman | 10 April 2019, 14:54:47 UTC | Merge branch 'release/3.0' of github.com:satijalab/seurat-private into release/3.0 | 10 April 2019, 14:54:47 UTC |
| 6fa73f6 | Paul Hoffman | 10 April 2019, 14:54:34 UTC | Merge pull request #1349 from ddiez/patch-1 Update utilities.R | 10 April 2019, 14:54:34 UTC |
| bfcbc0a | Paul Hoffman | 10 April 2019, 14:54:10 UTC | Merge pull request #1350 from ddiez/release/3.0 Update utilities.R: add ... argument to CellCycleScore() | 10 April 2019, 14:54:10 UTC |
| 6c02ab0 | Christoph Hafemeister | 10 April 2019, 13:28:32 UTC | Merge branch 'release/3.0' of https://github.com/satijalab/seurat-private into release/3.0 | 10 April 2019, 13:28:32 UTC |
| 9752109 | Christoph Hafemeister | 10 April 2019, 13:28:18 UTC | Make VariableFeaturePlot work with SCTransform workflow | 10 April 2019, 13:28:18 UTC |
| 399bedf | Diego Diez | 10 April 2019, 05:42:13 UTC | Update utilities.R Add `...` argument to `CellCycleScore()` in order to pass arguments to `AddModuleScore()`, such as `nbin`. Rationale is: I was running CellCycleScore() on a dataset and got error "Error: Insufficient data values to produce 24 bins.". So being able to set arguments in AddModuleScore from CellCycleScore could be useful. | 10 April 2019, 05:42:13 UTC |
| 309e5d5 | Diego Diez | 10 April 2019, 05:31:19 UTC | Update utilities.R Fix typo in doc. | 10 April 2019, 05:31:19 UTC |
| eff118d | Paul Hoffman | 10 April 2019, 00:36:54 UTC | Seurat v3.0.0.9100 - Address issues with CRAN checks | 10 April 2019, 00:36:54 UTC |
| 23a4b5b | Christoph Hafemeister | 09 April 2019, 22:34:32 UTC | Update SCTransform wrapper | 09 April 2019, 22:34:32 UTC |
| 517c83b | Christoph Hafemeister | 09 April 2019, 21:59:30 UTC | Add conserve.memory parameter to SCTransform; if TRUE we will never hold a full residual matrix in memory (only for variable features) | 09 April 2019, 21:59:30 UTC |
| eddebe8 | Andrew Butler | 09 April 2019, 20:49:12 UTC | Merge pull request #1335 from zeehio/feature/pca_total_variance Let RunPCA report total variance | 09 April 2019, 20:49:12 UTC |
| 327bf49 | Andrew Butler | 09 April 2019, 20:26:32 UTC | cleaner test output | 09 April 2019, 20:26:32 UTC |
| 1d891f9 | Paul Hoffman | 09 April 2019, 19:02:09 UTC | Merge branch 'release/3.0' of github.com:satijalab/seurat-private into release/3.0 | 09 April 2019, 19:02:09 UTC |
| 02e7932 | Paul Hoffman | 09 April 2019, 19:02:05 UTC | Merge branch 'release/3.0' of github.com:satijalab/seurat into release/3.0 | 09 April 2019, 19:02:05 UTC |
| 4e7580c | Paul Hoffman | 09 April 2019, 19:01:31 UTC | Add a slot parameter to FindMarkers | 09 April 2019, 19:01:31 UTC |
| 7abe34c | Paul Hoffman | 09 April 2019, 18:31:17 UTC | Merge pull request #1332 from BenjaminDoran/BenjaminDoran-patch-ReadH5AD Reads H5AD files with zeroed cols | 09 April 2019, 18:31:17 UTC |
| d602e93 | Andrew Butler | 09 April 2019, 17:41:46 UTC | ensure random seed is set in HTODemux | 09 April 2019, 17:41:46 UTC |
| bf7843f | Paul Hoffman | 09 April 2019, 16:29:56 UTC | Adjust as.sparse.H5Group to take dimensions into account | 09 April 2019, 16:29:56 UTC |
| 1642370 | Andrew Butler | 09 April 2019, 16:01:37 UTC | forgot to change name in test | 09 April 2019, 16:01:37 UTC |
| e49d9bb | Andrew Butler | 09 April 2019, 15:29:14 UTC | minor style fixes | 09 April 2019, 15:29:14 UTC |
| ba0641d | Paul Hoffman | 09 April 2019, 15:13:17 UTC | More fixes for the new dim.DimReduc functionality | 09 April 2019, 15:13:17 UTC |
| 8d646fc | Paul Hoffman | 09 April 2019, 15:02:28 UTC | devtools::document updated this | 09 April 2019, 15:02:28 UTC |
| 3bc5a69 | Paul Hoffman | 09 April 2019, 15:00:50 UTC | Address #1337 Fix issue with Loadings and JackStraw not working properly since we changed how dim.DimReduc and Loadings.DimReduc work | 09 April 2019, 15:00:50 UTC |
| 1c8fdc1 | Paul Hoffman | 09 April 2019, 14:48:33 UTC | Merge branch 'release/3.0' of github.com:satijalab/seurat into release/3.0 | 09 April 2019, 14:48:33 UTC |
| be7eecd | Paul Hoffman | 09 April 2019, 14:47:09 UTC | Replace FeatureLocator with CellSelector Can now set the identities of selected cells if a Seurat object is passed as well | 09 April 2019, 14:47:09 UTC |
| 31ba362 | Christoph Hafemeister | 09 April 2019, 14:43:59 UTC | devtools::document() changed this | 09 April 2019, 14:43:59 UTC |
| c537a9a | Christoph Hafemeister | 09 April 2019, 14:43:37 UTC | Set return.only.var.genes to TRUE in SCTransform | 09 April 2019, 14:43:37 UTC |
| 528a89d | Christoph Hafemeister | 09 April 2019, 14:40:44 UTC | Overhaul SCTransform to allow for three-step processing of data by sctransform package
If only variable genes are to be returned, the normalization is broken up into three steps: 1) get regularized models, 2) get residual variance for each gene 3) calculate residuals for only variable genes. Advantage of this is that the full residual matrix for all genes is never calculated. | 09 April 2019, 14:40:44 UTC |
| 5e473d3 | Christoph Hafemeister | 09 April 2019, 11:49:45 UTC | Make SCTransform always return gene attributes | 09 April 2019, 11:49:45 UTC |
| a89daa6 | Christoph Hafemeister | 09 April 2019, 10:12:59 UTC | Merge branch 'release/3.0' of https://github.com/satijalab/seurat into release/3.0 | 09 April 2019, 10:12:59 UTC |
| 304d189 | Andrew Butler | 09 April 2019, 03:18:05 UTC | fix subsetting DimReduc after dim switch | 09 April 2019, 03:18:05 UTC |
| 7413e89 | Paul Hoffman | 08 April 2019, 22:50:11 UTC | When removing an Assay, also remove associated DimReducs | 08 April 2019, 22:50:11 UTC |
| 0035c22 | Paul Hoffman | 08 April 2019, 19:03:07 UTC | Change how dim and dimnames work for DimReduc objects Both now pull from the embeddings matrix for their values ncol is now number of dimensions, colnames is now names of dimensions nrow is now number of cells, rownames is now names of cells Dimension information for loadings must now be called on Loadings matrix Change default Loadings matrix to unprojected, even if projected is present Add new Cells.DimReduc method to pull cell names for DimReducs | 08 April 2019, 19:03:07 UTC |
| 8a35517 | Paul Hoffman | 08 April 2019, 16:15:49 UTC | Showcase use of levels<- to reorder identity classes | 08 April 2019, 16:15:49 UTC |
| 6e33626 | Paul Hoffman | 08 April 2019, 15:03:48 UTC | Merge branch 'release/3.0' of github.com:satijalab/seurat-private into release/3.0 | 08 April 2019, 15:03:48 UTC |
| 037f275 | Paul Hoffman | 08 April 2019, 15:03:05 UTC | Use unprojected loadings by default | 08 April 2019, 15:03:05 UTC |
| 0e070c1 | Andrew Butler | 08 April 2019, 15:01:14 UTC | Fix initial ident setup when filtering cells (#1252) When min.features is set in CreateSeuratObject and cells are filtered out, the initial idents were still being set based on the original counts matrix. Fix to set on filtered assay object. | 08 April 2019, 15:01:14 UTC |
| db6e286 | Sergio Oller | 08 April 2019, 13:48:22 UTC | Let RunPCA report total variance | 08 April 2019, 14:09:12 UTC |
| 4fe5258 | Christoph Hafemeister | 08 April 2019, 08:52:30 UTC | Cleaning up SCTransform | 08 April 2019, 08:52:30 UTC |
| 28908f7 | BenjaminDoran | 06 April 2019, 15:14:13 UTC | style to repo convention | 06 April 2019, 15:14:13 UTC |
| f93b8be | BenjaminDoran | 06 April 2019, 14:55:58 UTC | reads in unfiltered h5ad with zeroed cols | 06 April 2019, 14:55:58 UTC |
| 71a3879 | Paul Hoffman | 05 April 2019, 22:36:23 UTC | Address #1329 AverageExpression now uses all assays by default Change parameter name to assays to reflect this | 05 April 2019, 22:36:23 UTC |
| 7deee26 | Paul Hoffman | 05 April 2019, 22:35:17 UTC | devtools::document back at it again, modifying files without changning anything | 05 April 2019, 22:35:17 UTC |
| be01cbe | Paul Hoffman | 05 April 2019, 22:16:44 UTC | Merge branch 'release/3.0' of github.com:satijalab/seurat into release/3.0 | 05 April 2019, 22:16:44 UTC |
| 75b8ac7 | Paul Hoffman | 05 April 2019, 21:40:32 UTC | Address #914 again Remove loomR from suggested Remove loomR repo Fix issue where devtools and remotes freak out because they're installing sugested packages when they aren't supposed to | 05 April 2019, 21:40:32 UTC |
| dec3086 | BenjaminDoran | 05 April 2019, 21:28:54 UTC | fix issue with columns of no expression in H5AD files | 05 April 2019, 21:28:54 UTC |
| 9e1a63a | Andrew Butler | 05 April 2019, 19:00:33 UTC | Merge branch 'release/3.0' of github.com:satijalab/seurat-private into release/3.0 | 05 April 2019, 19:00:33 UTC |
| cbf8759 | Andrew Butler | 05 April 2019, 18:52:22 UTC | Fix cut_number issue in AddModuleScore (#1227) If there were lots of duplicate values (usually arising from genes with zero average expression), this would cause problems for the cut_number function leading to the error: "insufficient data values to produce X bins". To solve this, add a small amount of random noise to the averages when determining the bins to break ties and allow for approximately equal sized bins to form. | 05 April 2019, 18:52:22 UTC |
| 7be9c39 | Paul Hoffman | 05 April 2019, 18:15:02 UTC | Check for assay presence when adding a DimReduc object | 05 April 2019, 18:15:02 UTC |
| 165d3de | Paul Hoffman | 05 April 2019, 18:01:11 UTC | Remove assay_generics.R | 05 April 2019, 18:01:11 UTC |
| 5632ddb | Paul Hoffman | 05 April 2019, 18:00:54 UTC | Merge branch 'release/3.0' of github.com:satijalab/seurat-private into release/3.0 | 05 April 2019, 18:00:54 UTC |
| 629cde1 | timoast | 05 April 2019, 18:00:35 UTC | fix error when loading v2 h5 files | 05 April 2019, 18:00:35 UTC |
| 0aa5c61 | Paul Hoffman | 05 April 2019, 17:58:45 UTC | Merge branch 'release/3.0' of github.com:satijalab/seurat-private into release/3.0 | 05 April 2019, 17:58:45 UTC |
| 4647e6f | Paul Hoffman | 05 April 2019, 17:56:42 UTC | FindClusters now stores identities in object[['seurat_clusters']] This allows easy retrival of latest cluster IDs This does not change other places FindClusters stores clustering results | 05 April 2019, 17:56:42 UTC |
| 9931804 | Rahul Satija | 05 April 2019, 17:56:25 UTC | When return.only.var.genes = T, SCTransform will remove non-variable genes from the @scale.data slot (as opposed to all slots) in the SCT assay | 05 April 2019, 17:56:25 UTC |
| 86a1b04 | Paul Hoffman | 05 April 2019, 17:46:49 UTC | VlnPlot can now pull features from the not-default assay | 05 April 2019, 17:46:49 UTC |
| 269694c | Paul Hoffman | 05 April 2019, 17:22:48 UTC | Show first 10 features for assays if HVF not set | 05 April 2019, 17:22:48 UTC |
| 0382279 | Paul Hoffman | 05 April 2019, 17:11:03 UTC | Add note about passing 'ident' to split or fetch identity classes | 05 April 2019, 17:11:03 UTC |
| fdb8d68 | Paul Hoffman | 05 April 2019, 16:41:11 UTC | Add ability to change which slot subsetting is done on | 05 April 2019, 16:41:11 UTC |
