| cfc2f29 | Paul Hoffman | 23 March 2018, 01:14:16 UTC | Add CRAN comments | 23 March 2018, 01:14:16 UTC |
| d2814e9 | Paul Hoffman | 22 March 2018, 23:18:00 UTC | Fix issue with FindAllMarkersNode | 22 March 2018, 23:18:00 UTC |
| 0688a4e | Paul Hoffman | 22 March 2018, 23:11:02 UTC | Merge branch 'develop' of github.com:satijalab/seurat-private into develop | 22 March 2018, 23:11:02 UTC |
| cfb3c51 | Paul Hoffman | 22 March 2018, 22:59:19 UTC | Keep doSNOW, fix FindAllMarkers | 22 March 2018, 23:08:43 UTC |
| 769a540 | Paul Hoffman | 22 March 2018, 22:59:19 UTC | Keep doSNOW, fix FindAllMarkers | 22 March 2018, 22:59:19 UTC |
| 1f80357 | Paul Hoffman | 22 March 2018, 22:43:19 UTC | Minor fix | 22 March 2018, 22:43:19 UTC |
| a036bda | Paul Hoffman | 22 March 2018, 22:37:38 UTC | Address #353 Change documentation for min.cells by splitting it into min.cells.group and min.cells.gene Remove min.cells from functions where it's unused | 22 March 2018, 22:37:38 UTC |
| 0d67a6a | Paul Hoffman | 22 March 2018, 22:14:13 UTC | Update documentation | 22 March 2018, 22:14:13 UTC |
| 9e0653a | Paul Hoffman | 22 March 2018, 22:05:25 UTC | Update version in README | 22 March 2018, 22:05:25 UTC |
| d4d4156 | Andrew Butler | 22 March 2018, 21:54:16 UTC | update NEWS and README | 22 March 2018, 21:54:16 UTC |
| c5f6d1a | Paul Hoffman | 22 March 2018, 21:47:50 UTC | Merge branch 'develop' of github.com:satijalab/seurat-private into develop | 22 March 2018, 21:47:50 UTC |
| 451cd3a | Paul Hoffman | 22 March 2018, 21:47:42 UTC | Update documentation | 22 March 2018, 21:47:42 UTC |
| 18b0c1e | Paul Hoffman | 22 March 2018, 21:46:54 UTC | Merge CRAN into develop | 22 March 2018, 21:46:54 UTC |
| 207c011 | Paul Hoffman | 22 March 2018, 21:30:26 UTC | Update version and date | 22 March 2018, 21:30:26 UTC |
| 05eeaab | Paul Hoffman | 22 March 2018, 21:04:41 UTC | Merge branch 'develop' of github.com:satijalab/seurat-private into develop | 22 March 2018, 21:04:41 UTC |
| d9bec75 | Andrew Butler | 22 March 2018, 20:57:08 UTC | Merge pull request #370 from aymanm/develop Adding multithreading support to Jackstraw function | 22 March 2018, 20:57:08 UTC |
| 9dddcf3 | Andrew Butler | 22 March 2018, 20:19:36 UTC | add optional progress bar, update docs | 22 March 2018, 20:19:36 UTC |
| 8fb26a1 | Andrew Butler | 22 March 2018, 19:47:14 UTC | fix issue with FindAllMarkers when no tests return results | 22 March 2018, 19:47:14 UTC |
| 2958eef | Andrew Butler | 21 March 2018, 20:45:17 UTC | remove now unnecessary parameter (nn_large) | 21 March 2018, 20:45:17 UTC |
| 5b87390 | Andrew Butler | 21 March 2018, 20:24:14 UTC | Merge branch 'feat/FastSNN' of github.com:satijalab/seurat-private into feat/FastSNN | 21 March 2018, 20:24:14 UTC |
| 913439c | Andrew Butler | 21 March 2018, 20:23:59 UTC | update NEWS | 21 March 2018, 20:23:59 UTC |
| 73fb530 | andrewwbutler | 21 March 2018, 05:28:27 UTC | add nn.eps parameter to FindClusters | 21 March 2018, 05:28:27 UTC |
| ac2ccd8 | Andrew Butler | 20 March 2018, 17:45:00 UTC | Merge branch 'feat/FastSNN' of github.com:satijalab/seurat-private into feat/FastSNN | 20 March 2018, 17:45:00 UTC |
| a67997c | Andrew Butler | 20 March 2018, 17:34:42 UTC | Merge branch 'develop' into feat/FastSNN | 20 March 2018, 17:34:42 UTC |
| 91ebd4c | Andrew Butler | 20 March 2018, 17:34:19 UTC | skip initial pca step when using Rtsne | 20 March 2018, 17:34:19 UTC |
| 454bd71 | aymanm | 19 March 2018, 15:01:39 UTC | fixed comment | 19 March 2018, 15:01:39 UTC |
| 09d7ad5 | aymanm | 19 March 2018, 15:00:35 UTC | fixed comment | 19 March 2018, 15:00:35 UTC |
| 9766692 | aymanm | 19 March 2018, 14:58:58 UTC | Add multithreading feature to Jackstraw function | 19 March 2018, 14:58:58 UTC |
| df54849 | Andrew Butler | 14 March 2018, 21:47:17 UTC | Merge branch 'develop' into feat/FastSNN | 14 March 2018, 21:47:17 UTC |
| 5828b22 | Andrew Butler | 14 March 2018, 21:39:19 UTC | simplify RunTSNE method choice with tsne.method parameter | 14 March 2018, 21:39:19 UTC |
| bbc6fc0 | Christoph Hafemeister | 14 March 2018, 21:30:28 UTC | use RANN::nn2 for NN calculation in BuildSNN instead of FNN::get.knn | 14 March 2018, 21:30:28 UTC |
| 9e49da4 | Andrew Butler | 14 March 2018, 18:55:49 UTC | Merge branch 'develop' into feat/FastSNN | 14 March 2018, 18:55:49 UTC |
| 2c8e746 | Andrew Butler | 14 March 2018, 18:55:29 UTC | speed up AddMetaData for large datasets | 14 March 2018, 18:55:29 UTC |
| e52cbe2 | Paul Hoffman | 13 March 2018, 22:42:19 UTC | Merge branch 'develop' of github.com:satijalab/seurat-private into develop | 13 March 2018, 22:42:19 UTC |
| 9291541 | Andrew Butler | 13 March 2018, 21:57:21 UTC | Merge pull request #358 from aymanm/develop Adding multithreading option to ScaleData/RegressOutResid | 13 March 2018, 21:57:21 UTC |
| 8dd9ba3 | Andrew Butler | 13 March 2018, 20:22:33 UTC | fix docs | 13 March 2018, 20:22:33 UTC |
| 9de5d2e | Andrew Butler | 13 March 2018, 19:38:50 UTC | add parallelization test | 13 March 2018, 19:38:50 UTC |
| 7e1187f | Andrew Butler | 13 March 2018, 19:37:55 UTC | add option to specify number of cores, minor formating changes | 13 March 2018, 19:37:55 UTC |
| a20ff03 | aymanm | 13 March 2018, 06:49:16 UTC | Adding multithreading option to ScaleData/RegressOutResid | 13 March 2018, 06:49:16 UTC |
| fca06b3 | Andrew Butler | 12 March 2018, 21:37:30 UTC | Merge branch 'develop' into feat/FastSNN | 12 March 2018, 21:37:30 UTC |
| 5934f5c | Christoph Hafemeister | 10 March 2018, 15:38:45 UTC | set RNG seed in WhichCells only if it is not NA | 10 March 2018, 15:38:45 UTC |
| 2b6ef9f | Christoph Hafemeister | 09 March 2018, 23:31:41 UTC | fixed bug that was introduced during code formatting; pointer in file needs to move 8 integers initially | 09 March 2018, 23:31:41 UTC |
| 5d71a4b | Rahul Satija | 06 March 2018, 19:16:38 UTC | Small fix | 06 March 2018, 19:16:38 UTC |
| 71f409a | Andrew Butler | 26 February 2018, 18:33:06 UTC | remove k.scale from SNN related functions | 26 February 2018, 18:33:06 UTC |
| 2e620dd | Paul Hoffman | 22 February 2018, 21:58:52 UTC | Merge branch 'develop' of github.com:satijalab/seurat into develop | 22 February 2018, 21:58:52 UTC |
| 71f32c6 | Paul Hoffman | 22 February 2018, 21:54:22 UTC | Clean up conflicting code | 22 February 2018, 21:54:22 UTC |
| aabb93e | Rahul Satija | 22 February 2018, 20:13:08 UTC | Merge branch 'develop' of https://github.com/satijalab/seurat-private into develop | 22 February 2018, 20:13:08 UTC |
| 8bc9e9c | Andrew Butler | 21 February 2018, 22:36:21 UTC | better way of removing zeros | 21 February 2018, 22:36:21 UTC |
| d4d5bc2 | Andrew Butler | 21 February 2018, 22:23:00 UTC | update write function so that it won't write zero edges | 21 February 2018, 22:23:00 UTC |
| f35a050 | Andrew Butler | 21 February 2018, 22:02:47 UTC | remove progress bar | 21 February 2018, 22:02:47 UTC |
| 27c1a87 | Andrew Butler | 21 February 2018, 21:18:46 UTC | add progress bar | 21 February 2018, 21:18:46 UTC |
| ef52897 | Rahul Satija | 21 February 2018, 17:11:27 UTC | Small updates | 21 February 2018, 17:11:27 UTC |
| 47b90fb | Andrew Butler | 20 February 2018, 22:13:59 UTC | redo ComputeSNN with matrix multiplication | 20 February 2018, 22:13:59 UTC |
| e3f9cff | Andrew Butler | 19 February 2018, 14:49:44 UTC | Merge pull request #296 from maehrlab/SubsetSeurat Add SubsetByPredicate | 19 February 2018, 14:49:44 UTC |
| 6acac29 | Eric Kernfeld | 15 February 2018, 03:54:25 UTC | Change name to SubsetByPredicate. | 15 February 2018, 03:54:25 UTC |
| 778a1f6 | Paul Hoffman | 14 February 2018, 18:54:17 UTC | Prepare 2.2.1 patch | 14 February 2018, 19:00:53 UTC |
| f4da9c6 | Andrew Butler | 14 February 2018, 18:37:31 UTC | swap MetaDE for metap, remove NMF dependency | 14 February 2018, 18:37:31 UTC |
| 3aa3f65 | andrewwbutler | 14 February 2018, 05:55:57 UTC | fix scaling issue with snn steps | 14 February 2018, 05:55:57 UTC |
| 7c44326 | Paul Hoffman | 13 February 2018, 22:30:15 UTC | Merge branch 'develop' of github.com:satijalab/seurat into develop | 13 February 2018, 22:30:15 UTC |
| af6906a | Paul Hoffman | 13 February 2018, 22:29:58 UTC | Update documentation | 13 February 2018, 22:29:58 UTC |
| 34aad41 | Paul Hoffman | 13 February 2018, 22:29:38 UTC | Add cells.highlight to DimPlot | 13 February 2018, 22:29:38 UTC |
| d5b9167 | Paul Hoffman | 13 February 2018, 22:12:52 UTC | Merge pull request #295 from 1j/develop Change to binning of genes when computing empirical fit to mean-CV relationship | 13 February 2018, 22:12:52 UTC |
| ba48970 | Paul Hoffman | 13 February 2018, 21:12:38 UTC | Merge pull request #272 from mukundvarma/master size.x.use not being passed to VlnPlot when x.lab.rot is also called | 13 February 2018, 21:12:38 UTC |
| 6de7b64 | Paul Hoffman | 13 February 2018, 21:04:15 UTC | Merge pull request #278 from gokceneraslan/patch-1 Fix spatial@final.prob variable name | 13 February 2018, 21:04:15 UTC |
| 594a59c | Paul Hoffman | 13 February 2018, 20:31:54 UTC | Merge branch 'develop' of github.com:satijalab/seurat-private into develop | 13 February 2018, 20:31:54 UTC |
| 8da0535 | Paul Hoffman | 13 February 2018, 20:20:01 UTC | Refactor, fix imports, add documentation | 13 February 2018, 20:20:01 UTC |
| e1f24a0 | Andrew Butler | 13 February 2018, 20:09:30 UTC | remove complete.cases check from ScaleData for large dataset compatibility (#279) | 13 February 2018, 20:09:59 UTC |
| a3367bb | Andrew Butler | 13 February 2018, 20:01:48 UTC | fix BuildClusterTree when using SNN (#177) | 13 February 2018, 20:01:48 UTC |
| 843f44b | Rahul Satija | 13 February 2018, 18:57:11 UTC | Small change to DimPlot that fixes legend title being displayed in DarkTheme | 13 February 2018, 18:57:11 UTC |
| 6450faa | Rahul Satija | 13 February 2018, 18:51:25 UTC | Merge branch 'develop' of https://github.com/satijalab/seurat-private into develop | 13 February 2018, 18:51:25 UTC |
| 8dab666 | Rahul Satija | 13 February 2018, 18:51:15 UTC | Added vector.friendly for FeaturePlot | 13 February 2018, 18:51:15 UTC |
| 30b1175 | Paul Hoffman | 13 February 2018, 18:43:06 UTC | Merge pull request #307 from leonfodoulian/patch-3 Plot gradient legends in SplitDotPlotGG() | 13 February 2018, 18:43:06 UTC |
| 75f90b0 | Paul Hoffman | 13 February 2018, 18:42:52 UTC | Merge pull request #306 from leonfodoulian/patch-1 Plot colour gradient legend | 13 February 2018, 18:42:52 UTC |
| 55a5833 | Paul Hoffman | 13 February 2018, 18:26:10 UTC | Merge branch 'develop' of github.com:satijalab/seurat-private into develop | 13 February 2018, 18:26:10 UTC |
| b624f63 | Paul Hoffman | 13 February 2018, 18:26:04 UTC | Prepare addition of SubsetSeurat via PR so original author gets credit on GitHub | 13 February 2018, 18:26:04 UTC |
| 08bedfe | Andrew Butler | 13 February 2018, 18:15:50 UTC | update NEWS | 13 February 2018, 18:15:50 UTC |
| 8237e7f | Andrew Butler | 13 February 2018, 18:07:06 UTC | finish merge | 13 February 2018, 18:07:06 UTC |
| c073fe3 | Andrew Butler | 13 February 2018, 18:05:30 UTC | fixes for CRAN, add examples | 13 February 2018, 18:05:30 UTC |
| 882f05c | Rahul Satija | 13 February 2018, 17:43:27 UTC | Merge branch 'develop' of https://github.com/satijalab/seurat-private into develop | 13 February 2018, 17:43:27 UTC |
| 108def6 | Rahul Satija | 13 February 2018, 17:43:13 UTC | Small fix | 13 February 2018, 17:43:13 UTC |
| cdb6832 | Paul Hoffman | 13 February 2018, 17:39:18 UTC | Update documentation and imports | 13 February 2018, 17:39:18 UTC |
| f5e262c | Rahul Satija | 13 February 2018, 17:28:44 UTC | Small fix | 13 February 2018, 17:28:44 UTC |
| 85e9718 | Rahul Satija | 13 February 2018, 17:27:58 UTC | Merge | 13 February 2018, 17:27:58 UTC |
| 6513550 | Rahul Satija | 13 February 2018, 17:15:17 UTC | Added vector.friendly to DimPlot | 13 February 2018, 17:15:17 UTC |
| 10e421f | Andrew Butler | 13 February 2018, 16:48:56 UTC | Merge branch 'develop' of github.com:satijalab/seurat-private into develop | 13 February 2018, 16:48:56 UTC |
| faa3d12 | Andrew Butler | 13 February 2018, 16:48:51 UTC | remove NMF dependency | 13 February 2018, 16:48:51 UTC |
| 206dc43 | Rahul Satija | 13 February 2018, 15:21:00 UTC | Added SubsetSeurat | 13 February 2018, 15:21:00 UTC |
| 22eef42 | Andrew Butler | 13 February 2018, 14:53:27 UTC | update docs | 13 February 2018, 14:53:27 UTC |
| b831ae3 | Rahul Satija | 12 February 2018, 23:59:04 UTC | Update to doublet confidence | 12 February 2018, 23:59:04 UTC |
| 4c60262 | Rahul Satija | 12 February 2018, 20:52:12 UTC | Doublet uncertainty | 12 February 2018, 20:52:12 UTC |
| 9795635 | Leon Fodoulian | 11 February 2018, 14:28:15 UTC | Update plotting.R | 11 February 2018, 14:28:15 UTC |
| 4235d58 | Leon Fodoulian | 11 February 2018, 14:27:40 UTC | Update plotting_internal.R | 11 February 2018, 14:27:40 UTC |
| ad52a7e | Leon Fodoulian | 11 February 2018, 14:22:28 UTC | Update plotting.R | 11 February 2018, 14:22:28 UTC |
| f656d52 | Leon Fodoulian | 11 February 2018, 14:12:38 UTC | Update plotting.R | 11 February 2018, 14:12:38 UTC |
| 63c2d10 | Leon Fodoulian | 11 February 2018, 14:09:54 UTC | Update plotting_internal.R | 11 February 2018, 14:09:54 UTC |
| e6c03f0 | Leon Fodoulian | 11 February 2018, 13:52:04 UTC | Plot gradient legends in SplitDotPlotGG() | 11 February 2018, 13:52:04 UTC |
| e788158 | Leon Fodoulian | 11 February 2018, 13:30:01 UTC | Plot colour gradient legend | 11 February 2018, 13:30:01 UTC |
| c045341 | Shiwei Zheng | 09 February 2018, 22:22:38 UTC | Fixed UpdateSeurat() for objects without dimensional reduction | 09 February 2018, 22:22:38 UTC |
| 844ed29 | Shiwei Zheng | 09 February 2018, 22:19:12 UTC | Added kmedoid clustering (clara) for initial HTO classification | 09 February 2018, 22:19:12 UTC |
| 52329d1 | Shiwei Zheng | 06 February 2018, 16:45:38 UTC | added assay.type argument (in case it's not named "HTO") | 06 February 2018, 16:45:38 UTC |
