| 87e2454 | Paul Hoffman | 11 February 2020, 21:52:16 UTC | Merge pull request #2605 from satijalab/develop Seurat v3.1.3 | 11 February 2020, 21:52:16 UTC |
| c772da1 | Paul Hoffman | 11 February 2020, 20:18:32 UTC | Fix tests | 11 February 2020, 20:18:32 UTC |
| 0324e13 | Paul Hoffman | 08 February 2020, 22:21:50 UTC | Fix documentation errors | 08 February 2020, 22:21:50 UTC |
| 53e3f4c | Paul Hoffman | 08 February 2020, 04:02:06 UTC | Merge pull request #255 from satijalab/release/3.1.3 Prep for CRAN release of 3.1.3 | 08 February 2020, 04:02:06 UTC |
| de97da4 | Andrew Butler | 07 February 2020, 23:05:36 UTC | add SDMTools to NEWS, typo fix | 07 February 2020, 23:05:36 UTC |
| 7cc3aea | Paul Hoffman | 07 February 2020, 22:52:23 UTC | Update CRAN comments | 07 February 2020, 22:52:23 UTC |
| 277f18e | Paul Hoffman | 07 February 2020, 22:47:46 UTC | Make SDMTools a suggested package instead of an imported one | 07 February 2020, 22:47:46 UTC |
| 0fed831 | Paul Hoffman | 07 February 2020, 19:39:28 UTC | Fix documentation errors | 07 February 2020, 19:39:28 UTC |
| 6fc9820 | Andrew Butler | 07 February 2020, 15:31:46 UTC | there isn't a weighted argument to graph_from_adj_list | 07 February 2020, 15:33:29 UTC |
| f53a1cb | Andrew Butler | 07 February 2020, 15:01:59 UTC | update DESCRIPTION, NEWS, README for CRAN release | 07 February 2020, 15:01:59 UTC |
| a9c939c | Paul Hoffman | 04 February 2020, 22:59:41 UTC | Merge pull request #2569 from amcdavid/master Link to sctransform methods that populate slots of SCTransform output | 04 February 2020, 22:59:41 UTC |
| 9ea819b | Paul Hoffman | 04 February 2020, 22:38:33 UTC | Style fixes | 04 February 2020, 22:38:33 UTC |
| 5553c76 | Paul Hoffman | 04 February 2020, 22:34:31 UTC | Merge branch 'develop' of github.com:satijalab/seurat | 04 February 2020, 22:34:31 UTC |
| 0d5e5e0 | Andrew Butler | 04 February 2020, 17:07:56 UTC | Merge pull request #253 from satijalab/feat/SCTtransfer_cca sct transfer cca | 04 February 2020, 17:07:56 UTC |
| 693bc8e | Andrew Butler | 04 February 2020, 16:59:22 UTC | bump develop version | 04 February 2020, 16:59:22 UTC |
| 9c8e1d6 | Andrew Butler | 04 February 2020, 16:41:35 UTC | avoid scaling in another LogNorm case for FindTransferAnchors | 04 February 2020, 16:41:35 UTC |
| 9df3ebc | Andrew Butler | 04 February 2020, 15:28:15 UTC | Merge branch 'develop' into feat/SCTtransfer_cca | 04 February 2020, 15:28:15 UTC |
| c9da7c2 | Paul Hoffman | 03 February 2020, 21:40:15 UTC | Merge pull request #250 from satijalab/fix/UnderscoreKeys bug fixes for keys with underscores | 03 February 2020, 21:40:15 UTC |
| 996dcaa | Andrew Butler | 03 February 2020, 21:25:15 UTC | bump develop version | 03 February 2020, 21:25:15 UTC |
| 58c2b14 | yuhanH | 03 February 2020, 18:35:34 UTC | sct transfer cca | 03 February 2020, 18:35:34 UTC |
| 6c854c3 | Paul Hoffman | 03 February 2020, 18:06:56 UTC | Merge branch 'develop' into fix/UnderscoreKeys | 03 February 2020, 18:06:56 UTC |
| 74e4a57 | Paul Hoffman | 03 February 2020, 18:05:41 UTC | Move fix from CreateDimReducObject to UpdateKey | 03 February 2020, 18:05:41 UTC |
| be561fd | Andrew Butler | 03 February 2020, 18:03:47 UTC | merge sync | 03 February 2020, 18:03:47 UTC |
| 0cd79ba | Andrew Butler | 03 February 2020, 17:54:12 UTC | Merge pull request #251 from satijalab/feat/UMAPInputChecks Better input checking for RunUMAP | 03 February 2020, 17:54:12 UTC |
| 2be8a58 | Andrew Butler | 03 February 2020, 17:48:21 UTC | bump develop version | 03 February 2020, 17:48:21 UTC |
| cd360a3 | Paul Hoffman | 03 February 2020, 16:49:28 UTC | Minor style fixes | 03 February 2020, 16:49:28 UTC |
| 549926f | Andrew McDavid | 03 February 2020, 16:14:30 UTC | Add links to sctransform methods that population slots of new object in SCTransform docs | 03 February 2020, 16:14:30 UTC |
| 9727d24 | Andrew Butler | 30 January 2020, 21:57:28 UTC | Better input checking for RunUMAP If fewer features (or reduced dimensions) than the number of UMAP components to compute are passed, stop and display more informative error message. For example, hopefully prevents confusion in cases like RunUMAP(object, dims = 10) | 30 January 2020, 21:57:28 UTC |
| 525798e | Andrew Butler | 30 January 2020, 21:29:57 UTC | bug fixes for keys with underscores When a key name with an underscore in the middle is passed to functions that generate DimReducs (e.g RunUMAP), the key gets truncated at the first underscore. Additionally, if it ends with a number (e.g. key.name = "umap_test2"), this causes bugs as the number at the end can get appended to the dimension number (e.g. dimension 1 becomes dimension 21). | 30 January 2020, 21:29:57 UTC |
| 45944a7 | Paul Hoffman | 23 January 2020, 21:55:11 UTC | Merge pull request #2538 from satijalab/fix/Sweep4 Add new Sweep internal function | 23 January 2020, 21:55:11 UTC |
| 950d661 | Andrew Butler | 23 January 2020, 21:30:28 UTC | bump develop version | 23 January 2020, 21:30:28 UTC |
| ea76245 | Andrew Butler | 23 January 2020, 21:29:59 UTC | Merge branch 'develop' into fix/Sweep4 | 23 January 2020, 21:29:59 UTC |
| 2f0bb6a | Paul Hoffman | 23 January 2020, 20:30:54 UTC | Add new Sweep internal function R v4 changes sweep to use captial X instead of lowercase x New wrapper function allows compatability with both R v3 sweep and v4 sweep | 23 January 2020, 20:30:54 UTC |
| c2c5bba | Andrew Butler | 22 January 2020, 19:02:40 UTC | Merge pull request #2440 from chlee-tabin/master Bug-fix of FindClusters Leiden algorithm | 22 January 2020, 19:02:40 UTC |
| 9800c3f | Andrew Butler | 22 January 2020, 17:55:01 UTC | bump develop version | 22 January 2020, 17:55:01 UTC |
| 3bbf89c | Andrew Butler | 22 January 2020, 17:03:12 UTC | Merge branch 'develop' of github.com:satijalab/seurat | 22 January 2020, 17:03:12 UTC |
| dbd5e60 | Paul Hoffman | 17 January 2020, 18:12:32 UTC | Merge pull request #240 from satijalab/fix/win_fast_tsne Add new system-agnostic Which function | 17 January 2020, 18:12:32 UTC |
| 9ea46bb | Andrew Butler | 17 January 2020, 18:00:46 UTC | bump develop version | 17 January 2020, 18:00:46 UTC |
| e9c4172 | Paul Hoffman | 17 January 2020, 17:36:50 UTC | Rename Which to SysExec | 17 January 2020, 17:36:50 UTC |
| 26d6d56 | Paul Hoffman | 17 January 2020, 17:25:14 UTC | Merge branch 'develop' into fix/win_fast_tsne | 17 January 2020, 17:25:14 UTC |
| b12ed36 | Paul Hoffman | 17 January 2020, 17:24:31 UTC | Fixes to Which | 17 January 2020, 17:24:31 UTC |
| 878e3f7 | Andrew Butler | 17 January 2020, 17:23:34 UTC | Merge pull request #246 from satijalab/fix/UpdateMetaData fill nFeature/nCount when converting 2 to 3 | 17 January 2020, 17:23:34 UTC |
| c17a08c | Paul Hoffman | 17 January 2020, 17:12:57 UTC | Bump develop version | 17 January 2020, 17:12:57 UTC |
| 3b89457 | Andrew Butler | 17 January 2020, 17:04:56 UTC | fill nFeature/nCount when converting 2 to 3 | 17 January 2020, 17:04:56 UTC |
| 7213e39 | chlee-tabin | 16 January 2020, 20:01:54 UTC | Merge pull request #1 from TomKellyGenetics/pr Changes to correct passing weights for Leiden | 16 January 2020, 20:01:54 UTC |
| 53f0ea8 | TomKellyGenetics | 16 January 2020, 02:58:50 UTC | add support for passing weight graphs to Leiden | 16 January 2020, 02:58:50 UTC |
| 1551108 | TomKellyGenetics | 16 January 2020, 02:52:46 UTC | Merge branch 'master' of https://github.com/chlee-tabin/seurat into pr | 16 January 2020, 02:52:46 UTC |
| 721a970 | Andrew Butler | 14 January 2020, 15:55:58 UTC | small refactor, make sure adj mat is weighted | 14 January 2020, 15:55:58 UTC |
| 518804f | Paul Hoffman | 10 January 2020, 23:00:07 UTC | Merge pull request #206 from satijalab/feat/Vlnplot_multigroup add multiple group in violin split plot | 10 January 2020, 23:00:07 UTC |
| e2db950 | Paul Hoffman | 10 January 2020, 22:54:40 UTC | Bump develop version | 10 January 2020, 22:54:40 UTC |
| 3f933f2 | yuhanH | 10 January 2020, 22:43:46 UTC | add documentation, remove redundant | 10 January 2020, 22:43:46 UTC |
| 97fa6f3 | Paul Hoffman | 10 January 2020, 22:27:43 UTC | Adjust style Start enabling use of preexisting code rather than duplicating it | 10 January 2020, 22:27:43 UTC |
| ced3096 | Paul Hoffman | 10 January 2020, 22:19:07 UTC | Merge branch 'develop' into feat/Vlnplot_multigroup | 10 January 2020, 22:19:07 UTC |
| 85714ae | Andrew Butler | 10 January 2020, 18:20:28 UTC | Merge pull request #245 from satijalab/fix/Read10XErrorMsg update file missing error messages in Read10X | 10 January 2020, 18:20:28 UTC |
| d064c0e | Andrew Butler | 10 January 2020, 17:34:53 UTC | merge | 10 January 2020, 17:34:53 UTC |
| 2354a4f | Andrew Butler | 10 January 2020, 17:33:00 UTC | Merge pull request #241 from satijalab/fix/KeepCols Retain nCount/nFeature cols after subset | 10 January 2020, 17:33:00 UTC |
| 692e050 | Paul Hoffman | 10 January 2020, 17:19:19 UTC | Bump develop version | 10 January 2020, 17:19:19 UTC |
| db8cb8a | Andrew Butler | 10 January 2020, 17:15:36 UTC | bump develop version | 10 January 2020, 17:15:36 UTC |
| 971fea5 | Andrew Butler | 10 January 2020, 17:11:55 UTC | update file missing error messages in Read10X | 10 January 2020, 17:11:55 UTC |
| 407cca5 | Andrew Butler | 09 January 2020, 20:09:34 UTC | Merge branch 'develop' into fix/KeepCols | 09 January 2020, 20:09:34 UTC |
| 7da0da9 | Paul Hoffman | 09 January 2020, 17:11:34 UTC | Merge pull request #242 from satijalab/fix/umap-features Enable uwot on feature matrix | 09 January 2020, 17:11:34 UTC |
| e8a8b07 | Paul Hoffman | 09 January 2020, 15:58:51 UTC | Bump develop version | 09 January 2020, 15:58:51 UTC |
| 9dfa738 | Andrew Butler | 09 January 2020, 15:11:28 UTC | Enable uwot on feature matrix Addresses satijalab/seurat#2466. uwot throws the error: "Sparse matrices are only supported as distance matrices" when given a feature matrix. This coerces to a dense matrix to handle that case. | 09 January 2020, 15:11:28 UTC |
| bf18585 | Andrew Butler | 03 January 2020, 17:19:10 UTC | Retain nCount/nFeature cols after subset | 03 January 2020, 17:19:10 UTC |
| 6a0cf80 | Andrew Butler | 03 January 2020, 16:57:14 UTC | Merge pull request #2469 from evolvedmicrobe/nd/fix_api Fix getEdges() Method of the Network Class | 03 January 2020, 16:57:14 UTC |
| d57cf7c | Andrew Butler | 03 January 2020, 16:25:01 UTC | Merge branch 'develop' into nd/fix_api | 03 January 2020, 16:25:01 UTC |
| ad91fe9 | Andrew Butler | 03 January 2020, 16:24:29 UTC | bump develop version | 03 January 2020, 16:24:29 UTC |
| 0204209 | Nigel Delaney | 02 January 2020, 18:53:00 UTC | Fix getEdges() Method of the Network Class The `getEdges` method was a public method of the `Network` class that allows users to obtain a copy of the Edges of a Network object. This method/interface was ported over from Java to C++ with a bug in it, though because the `getEdges` method is never called by either the Java or C++ version of the code, this bug had no effect on the current code. However, to improve the code and maintain it's similarity with the original Java version, it's probably worth fixing this unused method. The specific bug was that instead of filling an array from `start + value_1` to `start + value_2` with a constant value, it was filled from `start + value_1` to `end + value_2` with a constant value, which leads to unexpected behavior due to an array overflow. | 02 January 2020, 18:53:00 UTC |
| 89f6a71 | Paul Hoffman | 30 December 2019, 23:39:26 UTC | Add new system-agnostic Which function Addresses satijala/seurat#2464 | 30 December 2019, 23:39:26 UTC |
| a5caf34 | Andrew Butler | 20 December 2019, 20:20:47 UTC | Merge pull request #239 from satijalab/fix/DefaultColors Switch back to previous default color scheme | 20 December 2019, 20:20:47 UTC |
| bc21548 | Andrew Butler | 20 December 2019, 20:14:04 UTC | bump develop version | 20 December 2019, 20:14:04 UTC |
| 85fc0b4 | Andrew Butler | 20 December 2019, 16:51:47 UTC | switch back to default color scheme, leave parameter option | 20 December 2019, 16:51:47 UTC |
| bb3c8a6 | chlee-tabin | 18 December 2019, 00:43:22 UTC | Consistent behavior of Leiden clustering between v3.1.1 and v3.1.2 * preprocessing code to leiden algorithm input was changed between v3.1.1 and v3.1.2 producing different default behavior of FindCluster * this is to make it consistent to the previous version. | 18 December 2019, 00:43:22 UTC |
| 4c2192e | Paul Hoffman | 17 December 2019, 05:50:22 UTC | Merge pull request #2284 from Alanocallaghan/palettes Use palettes from pals package | 17 December 2019, 05:50:22 UTC |
| be2dbfd | Paul Hoffman | 17 December 2019, 05:28:32 UTC | Merge branch 'develop' of github.com:satijalab/seurat into palettes | 17 December 2019, 05:28:32 UTC |
| fe499e1 | Andrew Butler | 16 December 2019, 23:12:40 UTC | Merge pull request #2389 from troels/average_expression Don't materialize dense matrix in AverageExpression and FindMarkers | 16 December 2019, 23:12:40 UTC |
| f5a47ed | Andrew Butler | 16 December 2019, 22:03:58 UTC | update imports, bump develop version | 16 December 2019, 22:03:58 UTC |
| e78f3b3 | Andrew Butler | 16 December 2019, 21:57:37 UTC | Merge branch 'develop' of github.com:satijalab/seurat into average_expression | 16 December 2019, 21:57:37 UTC |
| 8c3d642 | Paul Hoffman | 16 December 2019, 20:40:39 UTC | Fix code sorting and documentation issues Export DiscretePalette Minor style fixes | 16 December 2019, 20:40:39 UTC |
| 03b551c | Paul Hoffman | 16 December 2019, 20:34:06 UTC | devtools::document updated this | 16 December 2019, 20:34:06 UTC |
| f5df241 | Paul Hoffman | 16 December 2019, 20:32:17 UTC | Merge branch 'develop' of github.com:satijalab/seurat into palettes | 16 December 2019, 20:32:17 UTC |
| 49a1be0 | satijalab | 13 December 2019, 20:42:25 UTC | Merge pull request #2416 from satijalab/develop Seurat v3.1.2 | 13 December 2019, 20:42:25 UTC |
| 9f57968 | satijalab | 12 December 2019, 21:13:56 UTC | Merge pull request #234 from satijalab/release/3.1.2 Prep for CRAN release of 3.1.2 | 12 December 2019, 21:13:56 UTC |
| 04ebc61 | Paul Hoffman | 12 December 2019, 21:06:57 UTC | Update cran-comments | 12 December 2019, 21:06:57 UTC |
| 933eca0 | Paul Hoffman | 12 December 2019, 17:30:38 UTC | Require UWOT v0.1.5 or higher See satijalab/seurat#2256 for more details | 12 December 2019, 17:30:38 UTC |
| 10eca22 | Andrew Butler | 12 December 2019, 14:37:47 UTC | fix CellCycleScoring to work with new names fix | 12 December 2019, 14:37:47 UTC |
| ce52f9c | Paul Hoffman | 11 December 2019, 21:47:42 UTC | Add biocViews to DESCRIPTION to facilitate installation of bioc dependencies | 11 December 2019, 21:47:42 UTC |
| 400266a | Paul Hoffman | 11 December 2019, 20:10:30 UTC | Update documentation | 11 December 2019, 20:10:30 UTC |
| 0933b42 | Andrew Butler | 11 December 2019, 19:37:52 UTC | Merge branch 'develop' into release/3.1.2 | 11 December 2019, 19:37:52 UTC |
| bab5af8 | Andrew Butler | 11 December 2019, 19:37:05 UTC | Merge pull request #224 from satijalab/fix/assignment Add checks for object name assignment | 11 December 2019, 19:37:05 UTC |
| bb3fc9f | Andrew Butler | 11 December 2019, 19:30:18 UTC | bump develop version | 11 December 2019, 19:30:18 UTC |
| ae699eb | Paul Hoffman | 10 December 2019, 19:51:46 UTC | Add RenameAssays | 10 December 2019, 19:51:46 UTC |
| 1448774 | Paul Hoffman | 10 December 2019, 16:30:57 UTC | Handle(ish) multiple objects being added at once | 10 December 2019, 16:30:57 UTC |
| 328f5c3 | Paul Hoffman | 10 December 2019, 16:28:39 UTC | Only run make.names when value != NULL | 10 December 2019, 16:28:39 UTC |
| 51c4fae | Paul Hoffman | 10 December 2019, 16:02:08 UTC | Merge branch 'develop' into fix/assignment | 10 December 2019, 16:02:08 UTC |
| 1c9f06a | Paul Hoffman | 10 December 2019, 15:57:44 UTC | Merge branch 'develop' into release/3.1.2 | 10 December 2019, 15:57:44 UTC |
| de47632 | Paul Hoffman | 10 December 2019, 15:57:22 UTC | Merge pull request #237 from satijalab/docs/runpca Update docs for RunPCA | 10 December 2019, 15:57:22 UTC |
| 166ce1c | timoast | 09 December 2019, 15:42:53 UTC | Fix typo | 09 December 2019, 15:42:53 UTC |
| be5e5c1 | Andrew Butler | 09 December 2019, 15:31:49 UTC | Merge branch 'develop' into fix/assignment | 09 December 2019, 15:31:49 UTC |
| 082409e | Andrew Butler | 09 December 2019, 15:30:14 UTC | Merge branch 'develop' into release/3.1.2 | 09 December 2019, 15:30:14 UTC |
