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  2. Graph
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  • cf41eec (HEAD -> devel, origin/master, origin/devel, origin/HEAD) bump x.y.z version to odd y following creation of RELEASE_3_20 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2024-10-29 10:29:05 -0400;
  • a10430b (origin/RELEASE_3_20, RELEASE_3_20) bump x.y.z version to even y prior to creation of RELEASE_3_20 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2024-10-29 10:29:05 -0400;
  • 9105069 bump x.y.z version to odd y following creation of RELEASE_3_19 branch by J Wokaty <jwokaty@users.noreply.github.com> 2024-04-30 11:07:02 -0400;
  • 2e8da38 (origin/RELEASE_3_19, RELEASE_3_19) bump x.y.z version to even y prior to creation of RELEASE_3_19 branch by J Wokaty <jwokaty@users.noreply.github.com> 2024-04-30 11:07:02 -0400;
  • a0c005c bump x.y.z version to odd y following creation of RELEASE_3_18 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2023-10-24 11:05:52 -0400;
  • 9166218 (origin/RELEASE_3_18, RELEASE_3_18) bump x.y.z version to even y prior to creation of RELEASE_3_18 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2023-10-24 11:05:52 -0400;
  • 5b19ac6 bump x.y.z version to odd y following creation of RELEASE_3_17 branch by J Wokaty <jwokaty@users.noreply.github.com> 2023-04-25 11:02:20 -0400;
  • a71e49a (origin/RELEASE_3_17, RELEASE_3_17) bump x.y.z version to even y prior to creation of RELEASE_3_17 branch by J Wokaty <jwokaty@users.noreply.github.com> 2023-04-25 11:02:20 -0400;
  • 3fa552f Merge remote-tracking branch 'upstream/devel' into develop by Kelly Street <street.kelly@gmail.com> 2023-03-29 12:36:15 -0700;
  • 3d0591d re-ran biocthis::use_bioc_github_action again, with local version of bioconductor, rather than devel by Kelly Street <street.kelly@gmail.com> 2023-03-29 11:58:37 -0700;
  • 6a60669 re-ran newer version of biocthis::use_bioc_github_action() by Kelly Street <street.kelly@gmail.com> 2023-03-29 11:45:30 -0700;
  • 89af8cf updated via biocthis::use_bioc_github_action by Kelly Street <street.kelly@gmail.com> 2023-03-29 11:36:37 -0700;
  • 82c5aba added section to vignette on slingshot::predict(). by Kelly Street <street.kelly@gmail.com> 2023-03-29 11:24:20 -0700;
  • b2726c3 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 11:17:56 -0400;
  • c594d05 (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 11:17:56 -0400;
  • ff0c3d1 added slingAvgPseudotime function that produces a single pseudotime vector, averaged across all lineages. by Kelly Street <street.kelly@gmail.com> 2022-06-17 14:54:31 -0400;
  • 1b24146 version bump to 2.5.1 by Kelly Street <street.kelly@gmail.com> 2022-05-23 13:40:20 -0400;
  • 5d8cedb Merge branch 'master' into develop by Kelly Street <street.kelly@gmail.com> 2022-05-23 12:53:56 -0400;
  • 4ca328a updated GHA workflow to use R 4.2, Bioc 3.15 by Kelly Street <street.kelly@gmail.com> 2022-05-23 12:26:57 -0400;
  • 9e22e8f added missing 'as.probs' argument to slingCurveWeights,SingleCellExperiment method. by Kelly Street <street.kelly@gmail.com> 2022-05-23 11:43:57 -0400;
  • 52ca75c 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 15:49:31 +0000;
  • fbf2297 (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 15:49:31 +0000;
  • cf69e1a account for potential numerical instability in predict(), per issue <a href="#180">#180</a> by Kelly Street <street.kelly@gmail.com> 2022-04-08 15:43:04 -0400;
  • b93c716 (origin/RELEASE_3_14, RELEASE_3_14) merged bug fix from origin/master, set RELEASE_3_14 version to 2.2.1 by Kelly Street <street.kelly@gmail.com> 2022-04-07 16:27:11 -0400;
  • 3b46a62 version bump for bug fix related to recent igraph update. by Kelly Street <street.kelly@gmail.com> 2022-04-07 16:24:31 -0400;
  • 6d6453a updated GitHub Actions workflow to use Bioconductor 3.14 by Kelly Street <street.kelly@gmail.com> 2022-04-04 17:27:53 -0400;
  • b10cdf3 slight modifications to getLineages: (1) removed unnecessary `X.original <- X` (relic of older versions), (2) subset X and clusterLabels when passing to createClusterMST, to avoid issues with unclustered cells (they create edge weights and cluster coordinates of NA, due to `clusters <- clusters / rowSums(clusters)`). modified tests to avoid warnings about colnames of SCE not matching rownames of RD. by Kelly Street <street.kelly@gmail.com> 2022-04-04 17:20:22 -0400;
  • 7c9da1b Merge branch 'master' into develop by Kelly Street <street.kelly@gmail.com> 2022-03-30 14:40:36 -0400;
  • 3d8ac11 merged updates from Bioconductor, added DelayedMatrixStats to 'Suggests', per issue #178. by Kelly Street <street.kelly@gmail.com> 2022-03-30 12:05:48 -0400;
  • 1ad9f42 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 16:45:07 +0000;
  • cb87b60 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 16:45:07 +0000;
  • 66b04b6 added reference to python implementation by Kelly Street <street.kelly@gmail.com> 2021-10-08 11:43:17 -0400;
  • 26fe838 changed chick-bioc.yml to (hopefully) run on release version of Bioconductor on linux checks by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-08-31 12:06:55 -0400;
  • 3295d00 changed GHA workflow to use R 4.1 (current release). Version bump to 2.1.1. by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-08-30 17:54:03 -0400;
  • 99a346e fixed bug in slingPseudotime,PseudotimeOrdering that would return nothing when na = FALSE. by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-08-30 17:06:03 -0400;
  • 74b9504 bump x.y.z version to odd y following creation of RELEASE_3_13 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-05-19 16:36:05 +0000;
  • ffcbc53 (origin/RELEASE_3_13, RELEASE_3_13) bump x.y.z version to even y prior to creation of RELEASE_3_13 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-05-19 16:36:05 +0000;
  • db7ddac changed the way we check for whether or not to skip the 3D plotting tests. Was "if" statements, now uses testthat::skip_if_not_installed and skip_on_os. by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-05-13 13:10:42 -0400;
  • 911d130 removed "quietly = TRUE" when checking for rgl availability in tests (per Vince's suggestion that this may make the problem easier to diagnose). version 1.99.14 by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-04-29 13:59:02 -0400;
  • 1849380 skip rgl-related tests on Mac (per Herve's suggestion on bioc-devel mailing list). Version bump to 1.99.13. by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-04-29 12:50:09 -0400;
  • eeaf83c removed redundant checks in getCurves, replaced with single check to verify that getLineages had been run. Added a test for that check. Version bump to 1.99.12. by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-04-14 12:21:19 -0400;
  • 62a6ca1 more tests, to hit error messages in plotting functions. version bump to 1.99.11 by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-04-13 11:24:32 -0400;
  • f20c195 reran devtools::document() to reflect changes in default value of approx_points by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-04-06 17:34:43 -0400;
  • 1265cba version bump to 1.99.10 by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-04-06 17:18:33 -0400;
  • a1878a4 changed default value of approx_points to NULL everywhere (it was still FALSE for slingshot()). Removed a redundant test from predict(). Added unit tests aimed at getCurves() and predict(). by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-04-06 17:17:26 -0400;
  • cd9b298 more unit tests for helper and conversion functions. Version bump to 1.99.9 by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-04-06 15:49:53 -0400;
  • f41ed9a resolved object type issue in tests, allowing them to actually hit some previously missed code in as.PseudotimeOrdering() by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-04-06 14:05:43 -0400;
  • de3e930 version bump to 1.99.8 by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-04-06 13:24:27 -0400;
  • 833f8cc added unit tests for slingshot() and getLineages(), mostly dealing with special cases and error handling by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-04-06 13:02:33 -0400;
  • 145f726 version bump to 1.99.7 by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-04-05 17:13:04 -0400;
  • b40957f fixed bug in storage of curve assignment weights for PseudotimeOrdering objects ("weights" assay wasn't updating after getLineages). Added tests for conversion functions. by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-04-05 17:11:34 -0400;
  • 4dbfd63 removed DelayedMatrixStats block, added install command beneath installation of BiocCheck, at line 182. by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-04-05 12:13:22 -0400;
  • 3624daf added manual installation of DelayedMatrixStats (block starting at line 191 in check-bioc.yml) by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-04-05 12:00:08 -0400;
  • 665b853 version bump to 1.99.4 by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-04-01 13:19:21 -0400;
  • f559be3 removed .travis.yml (no longer needed) by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-04-01 12:38:14 -0400;
  • 30c9b63 Merge pull request <a href="#123">#123</a> from HectorRDB/master by Kelly Street <street.kelly@gmail.com> 2021-03-31 12:28:50 -0400;
  • 769f755 Update AllHelperFunctions.R by Hector Roux de Bézieux <hector.rouxdebezieux@berkeley.edu> 2021-03-31 13:25:45 +0200;
  • 25fc566 updated NEWS.md by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-03-24 16:28:25 -0400;
  • 691b7c8 version to 1.99.3 (letting bioconductor handle 1 -> 2 transition) by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-03-24 16:21:45 -0400;
  • c20cb0b added detailed descriptions to slingParams() documentation. Version bump to 2.0.1. by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-03-24 16:16:15 -0400;
  • 51dec7f fixed warnings about functions being replaced. Changed (almost) all igraph function calls to igraph::function(), to avoid importing whole package, which had several conflicts. by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-03-24 15:39:34 -0400;
  • 6f010eb added "as.df" argument to slingMST and slingCurves, which will return the output as a data.frame for plotting via ggplot. by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-03-24 11:38:30 -0400;
  • 40ec792 /nocache by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-03-22 16:53:55 -0400;
  • 75ad5ac switched plot.SlingshotDataSet and lines.SlingshotDataSet to S3 (mirroring the princurve counterparts). Added imported packages to Imports in DESCRIPTION. Added documentation of use.median and times to getLineages and slingshot() explicitly import matrixStats by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-03-22 16:38:06 -0400;
  • 5b18bc4 changed check-bioc.yml, when installing dependencies via remotes::install_local, changed build_vignettes to FALSE. by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-03-20 22:28:23 -0400;
  • 2f7fd62 changed check-bioc.yml back to 'cache-v1' by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-03-20 22:10:23 -0400;
  • a1ba6ec added grDevices to Suggests and library(grDevices) in main vignette (for colorRampPalette). Added "import graphics" to lines.SlingshotDataSet, since that's where the generic seems to be from. by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-03-20 21:57:00 -0400;
  • 3f2123c changed check-bioc.yml cache-version to 'cache-v2' by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-03-19 17:48:16 -0400;
  • 9a568cb /nocache by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-03-18 19:44:25 -0400;
  • 70c4080 Merge branch 'develop' into trajectoryutils by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-03-18 19:40:19 -0400;
  • 1da4f18 removed it by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-03-18 19:33:14 -0400;
  • c35f226 double quotes by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-03-18 19:23:06 -0400;
  • 729d946 made it R_COMPILE_AND_INSTALL_PACKAGES: 'always' (added single quotes) by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-03-18 19:11:55 -0400;
  • 7a291d9 added "R_COMPILE_AND_INSTALL_PACKAGES: always" to check-bioc.yml, as per suggestion here: https://stackoverflow.com/questions/63965875/error-processing-vignette-quickstart-rmd-failed-with-diagnostics-there-is-no by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-03-18 18:55:34 -0400;
  • ada3d4c added NEWS.md, moved TrajectoryUtils to depends, since GHA seems to be having trouble installing its dependencies? by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-03-18 18:30:25 -0400;
  • f7ab00f removed DelayedMatrixStats (didn't help) by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-03-18 17:01:37 -0400;
  • e820884 changed version to 1.99.1 (for now). added DelayedMatrixStats to Suggests, because vignettes were failing. by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-03-18 16:41:51 -0400;
  • 23ed073 went through vignettes and modified as necessary to use PseudotimeOrdering objects. Updated code for clarity and some descriptions. Also fixed bug with the 'na' argument to 'slingPseudotime' (introduced recently). by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-03-18 15:55:39 -0400;
  • c9cc9c2 ran "use_bioc_github_action(biocdocker = "devel", testthat = TRUE, covr = TRUE)" to use the devel version of bioconductor in GHA checks by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-03-18 12:31:53 -0400;
  • 10bae6b re-ran use_bioc_github_action(testthat = TRUE, covr = TRUE) by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-03-17 16:47:04 -0400;
  • d004a75 Big update to incorporate TrajectoryUtils package. Default objects are now PseudotimeOrdering objects and getLineages is now basically a wrapper around createClusterMST. Other changes: removed plotGenePseudotime removed SDS subsetting functionality removed ape::mst and associated references removed "import matrixStats" from getLineages removed import grdevices from plot.SlingshotDataSet removed `lineages` argument from slingshot() removed excess "shrink = shrink" argument passing in slingshot methods removed colData - slingClusters, redundant kept colData - slingPseudotime_1 (for now, to not break old code) internal setter functions .slingParams<- and .slingCurves<- now only work with PseudotimeOrdering objects added conversion functions, as.SlingshotDataSet and as.PseudotimeOrdering modified omega argument to align with outgroup argument (createClusterMST) by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-03-17 14:52:34 -0400;
  • e1fe226 reran biocthis::use_bioc_github_action(testthat = TRUE) by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-01-20 16:21:20 -0500;
  • 65a8217 fixed some typos in the documentation. by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2021-01-15 10:17:52 -0500;
  • b1d9722 Merge remote-tracking branch 'upstream/master' by Kelly Street <kstreet@berkeley.edu> 2020-11-17 11:34:07 -0500;
  • c8dec30 replaced Travis CI badge with GitHub Actions badge by Kelly Street <street.kelly@gmail.com> 2020-11-16 20:52:04 -0500;
  • e866d53 changed github actions workflow to run covr and testthat by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2020-11-16 18:00:28 -0500;
  • 5bb4d69 ran biocthis::use_bioc_github_actions() to set up CI through GitHub Actions by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2020-11-16 17:20:37 -0500;
  • 63fad28 version bump to 1.9.1 by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2020-11-16 13:30:07 -0500;
  • 6e4ccfd properly passed the 'na' argument when calling slingPseudotime on a SingleCellExperiment by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2020-11-16 13:27:56 -0500;
  • cc4ca9e bump x.y.z version to odd y following creation of RELEASE_3_12 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-10-27 11:36:00 -0400;
  • cf8b399 (origin/RELEASE_3_12, RELEASE_3_12) bump x.y.z version to even y prior to creation of RELEASE_3_12 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-10-27 11:36:00 -0400;
  • af355df version bump to 1.7.3 by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2020-07-15 12:09:35 -0400;
  • da08821 revised main vignette to use tradeSeq rather than mgcv and updated description of omega argument. Changed DESCRIPTION and bibFile.bib to reflect changes in vignette. by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2020-07-15 12:03:10 -0400;
  • fb71214 modified tests to hit appropriate checks (some intended for the "has zero rows" check were first getting flagged by "nrow(X) must equal length(clusterLabels)") by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2020-07-07 15:56:01 -0400;
  • 6451db1 added getLineages unit test for case with separate trajectories, only one with a given starting cluster. by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2020-07-07 15:24:51 -0400;
  • ef1bee5 removed redundant checks in getLineages by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2020-07-07 14:57:23 -0400;
  • 0bad827 additional unit test for slingBranchGraph (special case of multiple lineages, 1 node, previously only tested in slingBranchID) by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2020-07-06 18:56:00 -0400;
  • 376e7cf added unit tests for special cases of slingBranchID and slingBranchGraph by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2020-07-06 18:31:55 -0400;
  • 7e99d71 version bump to 1.7.2 reflecting updates to the behavior of omega. Also a few new unit tests. by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2020-07-06 12:49:26 -0400;
  • d9fb59f additional tests for slingBranchID and slingBranchGraph, changed '>' to '>=' in slingBranchID. by Kelly Street <kstreet@root-pcs-MacBook-Air.local> 2020-07-03 13:11:34 -0400;