1. SGSeq
  2. Graph
Graph of SGSeq
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  • 756479a (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 10:39:42 -0400;
  • be443cf (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 10:39:42 -0400;
  • efd89b7 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 10:35:48 -0400;
  • 9d8c0f3 (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 10:35:48 -0400;
  • e5f17df 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 11:10:36 -0400;
  • dfa228e (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 11:10:36 -0400;
  • af6f09e 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 15:22:24 +0000;
  • a19e395 (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 15:22:24 +0000;
  • f79a2e3 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 16:17:06 +0000;
  • 9468314 (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 16:17:06 +0000;
  • b96f7d4 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 16:08:58 +0000;
  • d7ca914 (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 16:08:58 +0000;
  • ecc85e0 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 11:00:12 -0400;
  • d776538 (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 11:00:12 -0400;
  • 6c67388 changed author email address by ldg21 <ldgoldstein@gmail.com> 2020-10-14 12:36:26 -0700;
  • a6d1d97 fixed errors due to new mitochondrial chromosome in BSgenome.Hsapiens.UCSC.hg19 by Leonard Goldstein <goldstel@gene.com> 2020-08-18 11:24:34 -0700;
  • 82283b3 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 18:44:44 +0000;
  • 446fe43 (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 18:44:44 +0000;
  • 81952fd removed messages for debugging by Leonard Goldstein <goldstel@gene.com> 2020-03-30 16:20:14 -0700;
  • 893ff92 added messages for debugging by Leonard Goldstein <goldstel@gene.com> 2020-03-16 12:03:00 -0700;
  • 2d915bd added messages for debugging by Leonard Goldstein <goldstel@gene.com> 2020-03-13 10:35:38 -0700;
  • 0021314 added messages for debugging by Leonard Goldstein <goldstel@gene.com> 2020-03-11 12:05:16 -0700;
  • 4524b59 added messages for debugging by Leonard Goldstein <goldstel@gene.com> 2020-03-09 12:18:10 -0700;
  • 49a15e2 fixed error due to new setting on bioc devel builders by Leonard Goldstein <goldstel@gene.com> 2020-03-04 23:28:45 -0800;
  • 185f6ed added dependency R (>= 4.0) by Leonard Goldstein <goldstel@gene.com> 2020-03-04 13:21:53 -0800;
  • 1867535 resync with SummarizedExperiment 1.17.3 by Hervé Pagès <hpages@fredhutch.org> 2020-02-28 18:18:59 -0800;
  • 63cdf60 more efficient processing of terminal exons by ldg21 <ldgoldstein@gmail.com> 2019-11-01 16:24:47 -0700;
  • d5e87e8 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 13:38:26 -0400;
  • 8200c5f (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 13:09:05 -0400;
  • bba3386 Resync various serialized objects with S4Vectors 0.23.19 by Hervé Pagès <hpages@fredhutch.org> 2019-08-23 05:19:07 -0700;
  • 46ff3e9 SGSegments/SGVariants contain CompressedGRangesList instead of GRangesList by Hervé Pagès <hpages@fredhutch.org> 2019-05-13 16:06:59 -0700;
  • 1bd14e6 GenomicRanges_OR_GenomicRangesList is now defined in GenomicRanges package by Hervé Pagès <hpages@fredhutch.org> 2019-05-13 15:44:18 -0700;
  • bb335ae 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 12:11:52 -0400;
  • fd131cc (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 11:53:50 -0400;
  • ac7e0ff (origin/RELEASE_3_8, RELEASE_3_8) fixed bug in exportFeatures by ldg21 <ldgoldstein@gmail.com> 2018-12-18 17:38:39 -0800;
  • 4d31337 fixed bug in exportFeatures by ldg21 <ldgoldstein@gmail.com> 2018-12-18 17:26:44 -0800;
  • d560b73 added ImmunoOncology to biocViews field by ldg21 <ldgoldstein@gmail.com> 2018-12-07 17:15:29 -0800;
  • 7313933 added ImmunoOncology to biocViews field by ldg21 <ldgoldstein@gmail.com> 2018-12-07 17:02:09 -0800;
  • b4f02c2 bump x.y.z versions to odd y after creation of RELEASE_3_8 branch by vobencha <vobencha@gmail.com> 2018-10-30 11:54:33 -0400;
  • 9d7e6c8 bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch by vobencha <vobencha@gmail.com> 2018-10-30 11:41:55 -0400;
  • 1b81ad3 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;
  • b0613d3 (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 10:35:34 -0400;
  • 36c663a updated documentation by Leonard Goldstein <goldstel@gene.com> 2018-04-11 08:34:23 -0700;
  • 5dc1696 Add ellipsis to signature of the "updateObject" methods by Hervé Pagès <hpages@fredhutch.org> 2018-04-10 10:48:33 -0700;
  • fa27a5b updated code to keep up with bioc changes by Leonard Goldstein - Regular <goldstel@rescomp5001.gene.com> 2018-03-08 10:59:29 -0800;
  • c25b98d use html_document instead of defunct html_document2 by ldg21 <ldgoldstein@gmail.com> 2018-02-27 18:08:57 -0800;
  • c524cc1 reserialize GRangesList instances as CompressedGRangesList instances by Hervé Pagès <hpages@fredhutch.org> 2018-02-05 08:18:41 -0800;
  • eb6f88a replace calls to phead/ptail with calls to heads/tails by Hervé Pagès <hpages@fredhutch.org> 2018-01-24 21:12:48 -0800;
  • 32ffd97 oops, needs to be (>= x.y.z), not (x.y.z) by Hervé Pagès <hpages@fredhutch.org> 2018-01-21 17:33:19 -0800;
  • 1486b82 follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12 by Hervé Pagès <hpages@fredhutch.org> 2018-01-21 17:01:00 -0800;
  • e95b8df bump x.y.z versions to odd y after creation of RELEASE_3_6 branch by Hervé Pagès <hpages@fredhutch.org> 2017-10-30 12:53:49 -0400;
  • 1c0a60b (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 12:40:43 -0400;
  • e92e7c7 changed functions plotFeatures and plotVariants so top-right panel is reserved for user-defined plots by Leonard Goldstein <goldstel@gene.com> 2017-06-22 22:34:50 +0000;
  • 95aa812 GenomicRangesORGenomicRangesList was renamed GenomicRanges_OR_GenomicRangesList in rtracklayer 1.37.2 by Herve Pages <hpages@fhcrc.org> 2017-06-18 15:07:54 +0000;
  • beffaaa 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;
  • a2f8082 (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;
  • 66fe94b 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;
  • b7f5edc changes in vignette by Leonard Goldstein <goldstel@gene.com> 2017-04-23 20:51:50 +0000;
  • dfe93e0 updated DESCRIPTION by Leonard Goldstein <goldstel@gene.com> 2017-04-07 21:45:52 +0000;
  • d531ba4 changes in documentation and vignette by Leonard Goldstein <goldstel@gene.com> 2017-04-07 21:36:31 +0000;
  • b954841 version bump to trigger rebuild after changes in class definitions in S4Vectors by Leonard Goldstein <goldstel@gene.com> 2017-02-09 22:37:14 +0000;
  • 73e50c2 Bug fix - when plotting gene models using the geneName argument, splice-site-only models caused an error by Leonard Goldstein <goldstel@gene.com> 2016-12-03 02:06:13 +0000;
  • 9bf7cca (origin/RELEASE_3_4, RELEASE_3_4) Bug fix - when plotting gene models using the geneName argument, splice-site-only models caused an error by Leonard Goldstein <goldstel@gene.com> 2016-12-03 02:05:54 +0000;
  • e1b8e1c 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;
  • 826789f Creating branch for BioC 3.4 release by Herve Pages <hpages@fhcrc.org> 2016-10-17 19:00:47 +0000;
  • 6c15c7f 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;
  • 4dd33fb bug fix in findSGVariants() by Leonard Goldstein <goldstel@gene.com> 2016-10-08 19:10:50 +0000;
  • e18f1d7 (origin/RELEASE_3_3, RELEASE_3_3) bug fix in findSGVariants() by Leonard Goldstein <goldstel@gene.com> 2016-10-08 19:10:23 +0000;
  • 576d8fc bug fix - for certain SGVariants, closed5p/3p was incorrectly set to TRUE; this bug only affected complex variants not returned by findSGVariants() by default (i.e. for include = "default") by Leonard Goldstein <goldstel@gene.com> 2016-09-23 21:39:48 +0000;
  • df9cbe6 bug fix - for certain SGVariants, closed5p/3p was incorrectly set to TRUE; this bug only affected complex variants not returned by findSGVariants() by default (i.e. for include = "default") by Leonard Goldstein <goldstel@gene.com> 2016-09-23 21:38:23 +0000;
  • ba9ba84 bug fix - in rare cases findSGVariants() returned empty results despite variants present by Leonard Goldstein <goldstel@gene.com> 2016-09-16 18:11:55 +0000;
  • 3e082bf bug fix - in rare cases findSGVariants() returned empty results despite variants present by Leonard Goldstein <goldstel@gene.com> 2016-09-16 18:10:34 +0000;
  • 9313519 addressed performance issues introduced during bug fix by Leonard Goldstein <goldstel@gene.com> 2016-09-08 21:57:02 +0000;
  • c37731a addressed performance issues introduced during bug fix by Leonard Goldstein <goldstel@gene.com> 2016-09-08 21:56:11 +0000;
  • ef1787f amendment to previous commit by Leonard Goldstein <goldstel@gene.com> 2016-09-05 22:58:41 +0000;
  • 7ebb5df amendment to previous commit by Leonard Goldstein <goldstel@gene.com> 2016-09-05 22:58:13 +0000;
  • 4f3e131 Changes in SGSeq 1.7.9 - Bug fixes by Leonard Goldstein <goldstel@gene.com> 2016-09-05 19:31:56 +0000;
  • 06055e6 Changes in SGSeq 1.6.7 - Bug fixes by Leonard Goldstein <goldstel@gene.com> 2016-09-05 19:28:53 +0000;
  • 3a5f830 changes in propagateAnnotation by Leonard Goldstein <goldstel@gene.com> 2016-09-01 22:06:21 +0000;
  • 81f8e94 Changes in SGSeq 1.7.7 - Bug fixes by Leonard Goldstein <goldstel@gene.com> 2016-07-27 01:48:59 +0000;
  • 4609e23 Changes in SGSeq 1.6.6 - Bug fixes by Leonard Goldstein <goldstel@gene.com> 2016-07-27 01:45:09 +0000;
  • 39047bd bug fixes in annotate() and predictVariantEffects() by Leonard Goldstein <goldstel@gene.com> 2016-06-20 20:41:13 +0000;
  • 9d81313 bug fixes in annotate() and predictVariantEffects() by Leonard Goldstein <goldstel@gene.com> 2016-06-20 20:40:34 +0000;
  • 7d6dbd8 fixed bug in addSpliceSites() by Leonard Goldstein <goldstel@gene.com> 2016-06-18 07:55:57 +0000;
  • 2231fcd fixed bug in addSpliceSites() by Leonard Goldstein <goldstel@gene.com> 2016-06-18 07:54:53 +0000;
  • 1e44477 replace 'granges(from, TRUE)' with 'granges(from, use.mcols=TRUE)' by Herve Pages <hpages@fhcrc.org> 2016-06-17 08:03:28 +0000;
  • 52863fc replace 'granges(from, TRUE)' with 'granges(from, use.mcols=TRUE)' by Herve Pages <hpages@fhcrc.org> 2016-06-17 07:58:30 +0000;
  • 5f48b16 added citation information, modified vignette by Leonard Goldstein <goldstel@gene.com> 2016-06-16 01:59:36 +0000;
  • 520c953 added citation information, modified vignette by Leonard Goldstein <goldstel@gene.com> 2016-06-16 01:59:16 +0000;
  • f76bde8 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;
  • 356b4d0 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;
  • 78de5f2 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;
  • f10b76c 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;
  • 4a446cb bump version after creating 3.3 branch by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-03 21:30:44 +0000;
  • 9d0aca9 Creating branch for BioC 3.3 release. by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-03 21:26:31 +0000;
  • 5508962 Bump versions prior to creation of 3.3 branch by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-03 21:20:18 +0000;
  • a9fd4d1 minor changes in DESCRIPTION and vignette by Leonard Goldstein <goldstel@gene.com> 2016-05-02 20:42:33 +0000;
  • 894e316 changes in vignette and documentation by Leonard Goldstein <goldstel@gene.com> 2016-05-01 21:44:45 +0000;
  • c8f5044 added updateObject methods for SGVariants and SGVariantCounts by Leonard Goldstein <goldstel@gene.com> 2016-04-30 22:42:31 +0000;
  • 34d3fa4 updated NEWS file by Leonard Goldstein <goldstel@gene.com> 2016-04-28 19:04:01 +0000;