Graph ofcelda
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  • f9c0ddf5 (HEAD -> master, origin/master, origin/HEAD) bump x.y.z version to odd y following creation of RELEASE_3_16 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2022-11-01 11:19:55 -0400;
  • e912edd2 (origin/RELEASE_3_16, RELEASE_3_16) bump x.y.z version to even y prior to creation of RELEASE_3_16 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2022-11-01 11:19:55 -0400;
  • 46704790 Updated website and docs based on pkgdown v2 with newer version number. by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-10-22 15:01:13 -0400;
  • 9c5b773a Updated Matrix conversion calls to be compatible with Matrix v1.4-2 by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-10-21 22:00:54 -0400;
  • f94fd233 Updates to version number and NEWS by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-10-21 20:50:46 -0400;
  • 0d4c863b Fixed bug related to factors/integers for z/y cluster labels within internal functions by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-10-21 20:27:29 -0400;
  • bceb0050 Fixed bug with altExp usage in plotting cell annotation code by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-05-29 11:15:12 -0400;
  • c6b5bdd5 Merge branch 'master' into devel by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-05-01 09:30:59 -0400;
  • ab01b66e Version bump and update docs for BioC 3.15 by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-04-30 16:00:25 -0400;
  • 46c1fdc9 Fixed display names in feature plot in report by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-04-27 13:27:06 -0400;
  • 0c5da48b Fix in the report to work with displayName. by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-04-27 10:08:00 -0400;
  • 7c1bc8e0 bump x.y.z version to odd y following creation of RELEASE_3_15 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2022-04-26 15:55:58 +0000;
  • 366a243e (origin/RELEASE_3_15, RELEASE_3_15) bump x.y.z version to even y prior to creation of RELEASE_3_15 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2022-04-26 15:55:58 +0000;
  • c6cae496 Fixed bug where sample labels were not stored correctly when using recurrsive split. Updated report to handle plotting of character cell annotations without trying to convert to numeric by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-04-14 13:45:59 -0400;
  • 80145b1a Remove install commands in vignettes. Version bump by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-04-13 15:55:44 -0400;
  • e5d9f52b Updated plotRPC functions to use splines instead of rolling mean by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-04-13 14:39:31 -0400;
  • 1c267f1c Fixed bug in perplexity of celda_G where phi was being recalculated by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-04-11 18:51:45 -0400;
  • a662ab48 Removed ability to subsample counts matrix when calculating perplexity. This will take a much larger update where theta, probability of each cell population in each sample, will need to be calculated from new samples by predicting the population for each cell. by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-04-11 14:48:36 -0400;
  • c7cb8fdf merged from master by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-04-05 08:40:46 -0400;
  • 5182e42c Fixed max overlap warnings with ggrepel in plotDimReduceCluster by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-03-31 14:53:47 -0400;
  • d81a2664 Updated docs and news by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-03-31 14:23:12 -0400;
  • c9b11795 Added BiocCheck to Git Actions and changed dependency in standard check by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-03-30 12:10:47 -0400;
  • 7b1cff6d Minor decontX vignette update by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-03-30 08:14:38 -0400;
  • 86e72d6a Merge remote-tracking branch 'bioc/master' into devel by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-03-29 11:54:06 -0400;
  • df2f404c Updates to decontX vignette and minor change to a decontX plotting function by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-03-29 11:05:16 -0400;
  • 9d69d59a Merge branch 'devel' of https://github.com/campbio/celda into devel by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-03-28 16:41:49 -0400;
  • 7e5d8207 Added subsampling parameters for perplexity calculation to recursive split functions by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-03-28 08:00:25 -0400;
  • df4f3326 Merge pull request <a href="#363">#363</a> from yuan-yin-truly/devel by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-03-27 18:25:45 -0400;
  • 7d788c93 Moved Matrix and SingleCellExperiment to Depends to make sure these are loaded when using celda by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-03-25 16:25:48 -0400;
  • 32df2530 Seurat retrieve count matrix by yuan-yin-truly <76789185+yuan-yin-truly@users.noreply.github.com> 2022-03-24 17:43:40 -0400;
  • 3ad9a0cf Add on Seurat integration by yuan-yin-truly <76789185+yuan-yin-truly@users.noreply.github.com> 2022-03-24 16:59:38 -0400;
  • bd0e39b8 singleCellTK integration by yuan-yin-truly <76789185+yuan-yin-truly@users.noreply.github.com> 2022-03-24 16:48:02 -0400;
  • 90fd6eeb Add integration with Seurat by yuan-yin-truly <76789185+yuan-yin-truly@users.noreply.github.com> 2022-03-24 16:29:11 -0400;
  • d042875e Correct typo in vignette and stress background should only contain empty droplets by yuan-yin-truly <76789185+yuan-yin-truly@users.noreply.github.com> 2022-03-24 15:10:37 -0400;
  • 1adf441f Merge pull request <a href="#357">#357</a> from yuan-yin-truly/background_input_for_any_class_bugfixing by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-01-16 13:54:10 -0500;
  • e189c4c8 Resolve merging conflict by Yuan <76789185+yuan-yin-truly@users.noreply.github.com> 2022-01-15 14:34:57 -0500;
  • 940db02a Merge pull request <a href="#356">#356</a> from yuan-yin-truly/adding_background_batch by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2022-01-15 14:02:30 -0500;
  • 01490d1a Function description update by Yuan <76789185+yuan-yin-truly@users.noreply.github.com> 2022-01-14 21:34:13 -0500;
  • a5241c67 Fix the background input bug when the input class is not SingleCellExperiment by Yuan <76789185+yuan-yin-truly@users.noreply.github.com> 2022-01-14 20:17:29 -0500;
  • 351caa81 lintr style by Yuan <76789185+yuan-yin-truly@users.noreply.github.com> 2022-01-13 16:50:22 -0500;
  • 884a4e13 Add additional check on bgBatch by Yuan <76789185+yuan-yin-truly@users.noreply.github.com> 2022-01-13 16:39:18 -0500;
  • 8c4f6ee5 Update param description and adding a bgBatch check by Yuan <76789185+yuan-yin-truly@users.noreply.github.com> 2022-01-13 16:21:05 -0500;
  • 7f23e4cf Typo and small bug by Yuan <76789185+yuan-yin-truly@users.noreply.github.com> 2022-01-13 16:00:45 -0500;
  • f2c7a5b4 Correct typo by Yuan <76789185+yuan-yin-truly@users.noreply.github.com> 2022-01-13 15:54:23 -0500;
  • 27654944 Update commends by Yuan <76789185+yuan-yin-truly@users.noreply.github.com> 2022-01-13 14:22:13 -0500;
  • 2d27bde7 Update background check function to also update bgBatch when background needs to be updated by Yuan <76789185+yuan-yin-truly@users.noreply.github.com> 2022-01-13 14:20:44 -0500;
  • 28c62059 Finishing up adding background batch param by Yuan <76789185+yuan-yin-truly@users.noreply.github.com> 2022-01-13 14:03:11 -0500;
  • b6c904a5 Revise param description by Yuan <76789185+yuan-yin-truly@users.noreply.github.com> 2022-01-13 13:26:36 -0500;
  • 4d76f1d8 Adding bgBatch to each batch cycle inference workflow by Yuan <76789185+yuan-yin-truly@users.noreply.github.com> 2022-01-13 13:08:39 -0500;
  • d5f86efa Adding batchBackground parameter to function signature by Yuan <76789185+yuan-yin-truly@users.noreply.github.com> 2022-01-13 00:28:38 -0500;
  • b556d051 Adding bgBatch description by Yuan <76789185+yuan-yin-truly@users.noreply.github.com> 2022-01-13 00:16:34 -0500;
  • b735d3f0 Updated perplexity functions to be able to subsample cells or run on the original matrix. Also fixed bug when running calculating perplexity on a new counts matrix by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-12-31 20:03:13 -0500;
  • 3a89bf5a Updated version to match Bioconductor by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-12-28 14:47:07 -0500;
  • f7bccaa1 bump x.y.z version to odd y following creation of RELEASE_3_14 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-10-26 16:52:02 +0000;
  • fb720ad6 (origin/RELEASE_3_14, RELEASE_3_14) bump x.y.z version to even y prior to creation of RELEASE_3_14 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-10-26 16:52:02 +0000;
  • 7c5d27c9 Updated version, docs, nav bar, and NEWS by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-10-04 12:44:28 -0400;
  • 8698668e Fixed conflict by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-10-03 17:45:17 -0400;
  • c96bb98a Sample labels are stored in their original form by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-10-03 17:43:01 -0400;
  • 829b7775 updated decontX messages by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-10-01 17:06:40 -0400;
  • 588fa5c1 Merge pull request <a href="#348">#348</a> from yuan-yin-truly/devel by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-10-01 17:02:16 -0400;
  • 9d15f7b0 Style check by Yuan <76789185+yuan-yin-truly@users.noreply.github.com> 2021-10-01 11:27:46 -0400;
  • b6ef607d Speed up sparse matrix assignmnet by Yuan <76789185+yuan-yin-truly@users.noreply.github.com> 2021-10-01 00:19:10 -0400;
  • 45bbb34f Updated decontX messages by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-09-30 16:32:31 -0400;
  • 3396d5b9 Conslidated news files by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-09-29 21:19:39 -0400;
  • 9e761f88 Changed vignettes to html instead of pdf by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-09-29 21:14:49 -0400;
  • 4fdab030 Added the ability to return a list of heatmaps to 'moduleHeatmap'. This made the generation of module heatmaps in the report much quicker as the data does not have to be renormalized each time by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-09-26 14:26:49 -0400;
  • e47c11e8 Added direct installation of tinytex by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-09-26 14:21:40 -0400;
  • c1043913 Updated GHA workflow - moved tinytex install by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-09-21 12:28:51 -0400;
  • 6a55b243 Updated standard GHA check by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-09-21 08:46:16 -0400;
  • 1e583c0e Changed GHA to standard check by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-09-20 18:45:46 -0400;
  • d987670d Fixed some bugs in the reports including using correct assay for UMAP and tSNE generation by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-09-20 18:44:15 -0400;
  • a048197a Fixed bug related to factor order when recoding Z/Y by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-09-20 15:55:31 -0400;
  • 55895f8f Moved author order in DESCRIPTION by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-09-20 14:25:26 -0400;
  • c6fbb12c added titles and authors to articles by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-09-20 14:24:25 -0400;
  • 4b872b60 Added back in necessary 'suggests' packages by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-09-16 21:57:33 -0400;
  • 4efe68ef Fixed bug in checking background matrix by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-09-16 21:57:09 -0400;
  • 28b9671d Attempting to fix GHA install for linux by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-09-16 20:40:46 -0400;
  • ea799db7 Github actions testing by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-09-13 14:38:14 -0400;
  • bcd5950f fix bug in workflow by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-09-13 14:09:55 -0400;
  • 2eface17 testing install of bluster from GitHub for Actions R CMD check by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-09-13 13:58:01 -0400;
  • 6127451e Removed extra packages from the suggests of DESCRIPTION by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-09-12 15:41:23 -0400;
  • 290237e1 Added package to dependency install list to make vignette build by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-09-12 14:40:06 -0400;
  • 27ad2958 Added GitHub workflows and removed Travis yml by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-09-12 12:05:59 -0400;
  • 2dedaa56 Updated link in pkgdown by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-08-02 15:39:22 -0400;
  • 8fbd7eeb minor tweaks to pkgdown docs by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-07-19 13:40:48 -0400;
  • c7f58240 Fixed lints by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-07-19 09:17:02 -0400;
  • a520debd Addition of pkgdown docs. Some tweaks to vignettes by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-07-18 19:47:16 -0400;
  • b74cac3f Fixed bugs when input is a sparse matrix by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-07-17 09:56:39 -0400;
  • 470ab87b Adjustments to automatic rowFonSize in moduleHeatmap when many modules are selected by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-07-16 17:07:14 -0400;
  • 3cc8a1bb Enabled celda_C/G/CG functions to take in a sparse matrix as input not in an SCE by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-07-16 16:29:36 -0400;
  • ddd46f0c Fixed typos in decontX vignette by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-07-16 16:11:19 -0400;
  • 1cb1db49 Fixed bug in featureModuleTable with displayName by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-07-16 16:09:35 -0400;
  • ee373e48 removed non-matching genesthat produced NA from plotDimReduceFeature by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-07-16 16:02:38 -0400;
  • 9b62c139 Changed dim reduce plotting so that the colnames of the reducedDim object will be displayed on the plot by default. Also added package refs in perplexity functions. by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-07-15 16:24:30 -0400;
  • eb67cf09 fixed warning message in plotRPC by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-07-10 14:13:39 -0400;
  • 6327331c Updated featureModuleLookup to be able to search rowData by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-07-10 09:47:41 -0400;
  • 3f9b2c76 Replaced donttest with dontrun to fix notes. Added missing package reference by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-07-07 16:10:08 -0400;
  • 01138e36 Minor change to way calculateUMAP is called from scater to improve speed and get around a potential error by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-07-07 13:25:05 -0400;
  • 7858987e Fixed bug in cG_CalcGibbsProbY that occured when numeric values in the matrix are not integers. Some input parameters were still typed at IntegerVector/Matrix and needed to be converted to NumericVector/Matrix by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-07-07 11:30:48 -0400;
  • e71856d0 Merge branch 'master' into devel by Joshua D. Campbell <joshua.d.campbell@gmail.com> 2021-07-07 09:32:54 -0400;