1. BubbleTree
  2. Graph
Graph of BubbleTree
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  • 56d4a11 (HEAD -> devel, origin/master, origin/devel, origin/HEAD) 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 10:41:33 -0400;
  • eea5b5e (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 10:41:33 -0400;
  • d9fcd6c 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 10:37:41 -0400;
  • 8686dde (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 10:37:41 -0400;
  • 20d9d74 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 11:11:07 -0400;
  • a9640da (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 11:11:07 -0400;
  • eb7e17d 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 15:23:48 +0000;
  • e421c4f (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 15:23:48 +0000;
  • 26a7104 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 16:18:49 +0000;
  • c74ad0d (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 16:18:49 +0000;
  • 4d34b1d 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 16:11:10 +0000;
  • d94bc48 (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 16:11:10 +0000;
  • 2f0e37d 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 11:02:36 -0400;
  • e891780 (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 11:02:36 -0400;
  • 50dd6a4 bump x.y.z version to odd y following creation of RELEASE_3_11 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-04-27 18:46:47 +0000;
  • 477c605 (origin/RELEASE_3_11, RELEASE_3_11) bump x.y.z version to even y prior to creation of RELEASE_3_11 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-04-27 18:46:47 +0000;
  • d694392 bump x.y.z version to odd y after creation of RELEASE_3_10 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2019-10-29 13:38:59 -0400;
  • 4929476 (origin/RELEASE_3_10, RELEASE_3_10) bump x.y.z version to even y prior to creation of RELEASE_3_10 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2019-10-29 13:09:09 -0400;
  • 629b602 Making sure that the %in% generic is imported from BiocGenerics by Hervé Pagès <hpages@fredhutch.org> 2019-10-03 07:50:29 -0700;
  • f4b5d81 bump x.y.z versions to odd y after creation of RELEASE_3_9 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2019-05-02 12:12:18 -0400;
  • 7c64327 (origin/RELEASE_3_9, RELEASE_3_9) bump x.y.z versions to even y prior to creation of RELEASE_3_9 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2019-05-02 11:53:53 -0400;
  • 90efc88 - updated dplyr filter call to satisify new dplyr 0.8.0 requirements in RBD.R - fixed a bug with the rmarkdown in BubbleTree-vignette.Rmd by Creasy, Todd <creasyt@medimmune.com> 2019-01-04 10:51:02 -0500;
  • 67689d5 fixed version number by Creasy, Todd <creasyt@medimmune.com> 2018-11-20 11:09:33 -0500;
  • 2fd7274 updated R req to 3.5; upticked new release number by Creasy, Todd <creasyt@medimmune.com> 2018-11-20 11:08:31 -0500;
  • 8165744 uptick the version by Creasy, Todd <creasyt@medimmune.com> 2018-11-19 22:36:40 -0500;
  • 35d7904 remove lengths() import from BiocGenerics by Creasy, Todd <creasyt@medimmune.com> 2018-11-19 22:21:14 -0500;
  • 95545c9 bump x.y.z versions to odd y after creation of RELEASE_3_8 branch by vobencha <vobencha@gmail.com> 2018-10-30 11:54:34 -0400;
  • 4eeb280 (origin/RELEASE_3_8, RELEASE_3_8) bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch by vobencha <vobencha@gmail.com> 2018-10-30 11:41:56 -0400;
  • 8498db3 bump x.y.z versions to odd y after creation of RELEASE_3_7 branch by vobencha <valerie.obenchain@roswellpark.org> 2018-04-30 10:41:40 -0400;
  • 9cc358b (origin/RELEASE_3_7, RELEASE_3_7) bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch by vobencha <valerie.obenchain@roswellpark.org> 2018-04-30 10:35:35 -0400;
  • e3136a2 bump x.y.z versions to odd y after creation of RELEASE_3_6 branch by Hervé Pagès <hpages@fredhutch.org> 2017-10-30 12:54:05 -0400;
  • 874d672 (origin/RELEASE_3_6, RELEASE_3_6) bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch by Hervé Pagès <hpages@fredhutch.org> 2017-10-30 12:40:49 -0400;
  • 7d68080 updated test data file allRBD.lst.RData so the demo works properly; removed line that changes elementMetadata to dataframe as it will already be a dataframe now by Todd Creasy <creasyt@medimmune.com> 2017-05-08 14:46:27 +0000;
  • 3c8c880 bump x.y.z versions to odd y after creation of 3_5 branch by Herve Pages <hpages@fhcrc.org> 2017-04-24 19:50:57 +0000;
  • 2f97875 (origin/RELEASE_3_5, RELEASE_3_5) Creating branch for BioC 3.5 release by Herve Pages <hpages@fhcrc.org> 2017-04-24 19:45:44 +0000;
  • dd9cf27 bump x.y.z versions to even y prior to creation of 3_5 branch by Herve Pages <hpages@fhcrc.org> 2017-04-24 19:25:24 +0000;
  • 5319a09 updated to new version by Todd Creasy <creasyt@medimmune.com> 2017-02-28 20:25:10 +0000;
  • 1267ecb check first if .Object@result$prev is NA (pp) assign colnames to predFit@config$xypGrid if the dataframe is empty by Todd Creasy <creasyt@medimmune.com> 2017-02-28 20:24:31 +0000;
  • 326f72e Removed "rainbow" function as it relies on the rgl packages that causes a warning on headless hosts by Todd Creasy <creasyt@medimmune.com> 2017-02-23 19:34:46 +0000;
  • f4e5851 updated maintainers by Todd Creasy <creasyt@medimmune.com> 2017-02-23 15:08:06 +0000;
  • 25e8129 Updated to new version after bug fix in BTreePredictor by Todd Creasy <creasyt@medimmune.com> 2017-02-22 21:09:33 +0000;
  • 1a73c7c bump x.y.z versions to odd 'y' after creation of 3_4 branch by Herve Pages <hpages@fhcrc.org> 2016-10-17 19:10:43 +0000;
  • ee6abf2 (origin/RELEASE_3_4, RELEASE_3_4) Creating branch for BioC 3.4 release by Herve Pages <hpages@fhcrc.org> 2016-10-17 19:00:47 +0000;
  • 6386eb6 bump x.y.z versions to even 'y' prior to creation of 3_4 branch by Herve Pages <hpages@fhcrc.org> 2016-10-17 18:45:06 +0000;
  • cb3f0a9 fixed calculation of purity when number of somatic snps is low by Todd Creasy <creasyt@medimmune.com> 2016-06-21 15:54:27 +0000;
  • b9dff7c fixed calculation of purity when number of somatic snps is low by Todd Creasy <creasyt@medimmune.com> 2016-06-21 15:53:44 +0000;
  • 251ea58 removed comment by Todd Creasy <creasyt@medimmune.com> 2016-06-09 19:40:08 +0000;
  • 79d74cd updated documentation by Todd Creasy <creasyt@medimmune.com> 2016-05-31 13:30:14 +0000;
  • 403a3eb (origin/RELEASE_3_3, RELEASE_3_3) Version bump to trigger package rebuilding now that purl()'ing issue has been correctly identified. knitr does not create purl()'ed (Stangle equivalent) .R files if _R_CHECK_TIMINGS_ is set, which the build system was setting. Now it's not set, so these .R files are now created. See https://github.com/yihui/knitr/issues/1212 for more. by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-15 20:18:19 +0000;
  • 4a7e552 Version bump to trigger package rebuilding now that purl()'ing issue has been correctly identified. knitr does not create purl()'ed (Stangle equivalent) .R files if _R_CHECK_TIMINGS_ is set, which the build system was setting. Now it's not set, so these .R files are now created. See https://github.com/yihui/knitr/issues/1212 for more. by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-15 20:14:22 +0000;
  • aaea2e9 Bump version of all packages that use knitr for vignettes. This is because of an issue (now fixed) in knitr which failed to create purl()'ed R files from vignette sources and include them in the package. This version bump will cause these packages to propagate with those R files included. by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-11 23:15:25 +0000;
  • 35ebc97 Bump version of all packages that use knitr for vignettes. This is because of an issue (now fixed) in knitr which failed to create purl()'ed R files from vignette sources and include them in the package. This version bump will cause these packages to propagate with those R files included. by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-11 23:05:31 +0000;
  • 08b2a8e bump version after creating 3.3 branch by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-03 21:30:44 +0000;
  • 62fc557 Creating branch for BioC 3.3 release. by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-03 21:26:31 +0000;
  • f6c4456 Bump versions prior to creation of 3.3 branch by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-03 21:20:18 +0000;
  • 020c537 updated vignette with proper syntax added specific function used in gridExtra by Todd Creasy <creasyt@medimmune.com> 2016-04-21 18:55:19 +0000;
  • 1d2e9a0 Added more documentation by Todd Creasy <creasyt@medimmune.com> 2016-04-21 17:45:38 +0000;
  • 5139a71 (origin/RELEASE_3_2, RELEASE_3_2) ggplot2 backports by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-01-31 00:29:21 +0000;
  • 498c288 remove rgl dependency by Todd Creasy <creasyt@medimmune.com> 2016-01-25 13:26:29 +0000;
  • 48896e8 removed requirement on rgl by Todd Creasy <creasyt@medimmune.com> 2016-01-25 12:46:37 +0000;
  • 6d42b2d fixed some build errors by Todd Creasy <creasyt@medimmune.com> 2016-01-22 12:13:55 +0000;
  • 3e86bc6 updates to avoid NAMESPACE conflicts by Todd Creasy <creasyt@medimmune.com> 2016-01-19 17:45:53 +0000;
  • c33ed7d updates to deal with situations where the sequence names are integers rather than "chr3", etc by Todd Creasy <creasyt@medimmune.com> 2016-01-07 22:09:51 +0000;
  • adb2305 updated fill color scale to account for datasets that have >25 seqnames by Todd Creasy <creasyt@medimmune.com> 2016-01-05 19:59:18 +0000;
  • 18aac93 removed unused parameter by Todd Creasy <creasyt@medimmune.com> 2016-01-05 18:40:39 +0000;
  • bb3ec92 updated to 2.1.6 by Todd Creasy <creasyt@medimmune.com> 2016-01-05 17:56:03 +0000;
  • 194e381 updated het.cnt default to 1 by Todd Creasy <creasyt@medimmune.com> 2016-01-05 17:53:34 +0000;
  • 0baeaaf changed a "0" value to NA by Todd Creasy <creasyt@medimmune.com> 2016-01-05 17:52:50 +0000;
  • 5eca732 updated geom_text to use fontface by Todd Creasy <creasyt@medimmune.com> 2016-01-05 17:51:03 +0000;
  • 95bad1b updated citation and example file by Todd Creasy <creasyt@medimmune.com> 2015-12-08 20:52:18 +0000;
  • 195739f updated makeRBD examples and the ploidy/purity is now printed out by Todd Creasy <creasyt@medimmune.com> 2015-12-08 19:28:05 +0000;
  • b8290c6 uptick of version by Todd Creasy <creasyt@medimmune.com> 2015-11-25 16:42:35 +0000;
  • e42eab3 updated docs by Todd Creasy <creasyt@medimmune.com> 2015-11-25 16:35:32 +0000;
  • d729dc5 allow predictions from a user-provided sample by Todd Creasy <creasyt@medimmune.com> 2015-11-25 16:31:09 +0000;
  • 989e547 updated with required package by Todd Creasy <creasyt@medimmune.com> 2015-11-24 20:31:18 +0000;
  • 19929e4 updated required packages by Todd Creasy <creasyt@medimmune.com> 2015-11-24 20:19:42 +0000;
  • 1b4002b updated docs by Todd Creasy <creasyt@medimmune.com> 2015-11-24 20:17:19 +0000;
  • 4c1fb7f fixed makeRBD to return correct object and plot the bubbletree by Todd Creasy <creasyt@medimmune.com> 2015-11-24 20:16:00 +0000;
  • 131aaa1 updated docs by Todd Creasy <creasyt@medimmune.com> 2015-11-18 13:11:49 +0000;
  • 30e94eb updated docs by Todd Creasy <creasyt@medimmune.com> 2015-11-18 12:21:07 +0000;
  • d6b23c5 updated docs by Todd Creasy <creasyt@medimmune.com> 2015-11-18 05:03:21 +0000;
  • 7c1ced6 upated docs by Todd Creasy <creasyt@medimmune.com> 2015-11-18 04:57:19 +0000;
  • 7e6cf59 updated vignette by Todd Creasy <creasyt@medimmune.com> 2015-11-18 04:49:34 +0000;
  • e43d00f moved test data to data/ by Todd Creasy <creasyt@medimmune.com> 2015-11-18 04:47:48 +0000;
  • 828416f moved data files to data/ by Todd Creasy <creasyt@medimmune.com> 2015-11-18 04:47:16 +0000;
  • 1cb014b updated docs by Todd Creasy <creasyt@medimmune.com> 2015-11-18 04:36:53 +0000;
  • 80b1e50 updated docs by Todd Creasy <creasyt@medimmune.com> 2015-11-18 04:26:08 +0000;
  • 4b8be89 updated docs by Todd Creasy <creasyt@medimmune.com> 2015-11-18 04:10:53 +0000;
  • d7ea887 updated docs by Todd Creasy <creasyt@medimmune.com> 2015-11-18 03:50:06 +0000;
  • 3121df5 updated docs by Todd Creasy <creasyt@medimmune.com> 2015-11-18 03:34:31 +0000;
  • 4d81cb4 updated docs by Todd Creasy <creasyt@medimmune.com> 2015-11-18 03:32:31 +0000;
  • 8029bc1 updated vignette by Todd Creasy <creasyt@medimmune.com> 2015-11-18 03:05:22 +0000;
  • 9d23b6e moved some files around to correct locations by Todd Creasy <creasyt@medimmune.com> 2015-11-18 03:02:34 +0000;
  • 09a9643 updated docs by Todd Creasy <creasyt@medimmune.com> 2015-11-18 02:54:58 +0000;
  • 2e22e94 removed debug statement added required library e1071 by Todd Creasy <creasyt@medimmune.com> 2015-11-18 02:29:30 +0000;
  • f190993 small change by Todd Creasy <creasyt@medimmune.com> 2015-11-18 02:13:41 +0000;
  • dd92386 updated with new RBD class to create a RBD object from cnv.gr and snp.gr by Todd Creasy <creasyt@medimmune.com> 2015-11-18 02:10:40 +0000;
  • d9fdc9e updated version number (again) by Todd Creasy <creasyt@medimmune.com> 2015-10-29 16:35:46 +0000;
  • 2e0595f updated version number by Todd Creasy <creasyt@medimmune.com> 2015-10-29 16:32:52 +0000;
  • b8eb089 updated maintainers and email addresses by Todd Creasy <creasyt@medimmune.com> 2015-10-29 16:30:24 +0000;