1. R453Plus1Toolbox
  2. Graph
Graph of R453Plus1Toolbox
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  • 225ebbc (HEAD -> devel, origin/master, origin/devel, origin/HEAD) 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 10:18:15 -0400;
  • 4064694 (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 10:18:15 -0400;
  • 7b302c5 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 11:05:23 -0400;
  • 93bf3f8 (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 11:05:23 -0400;
  • 79327f0 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 15:06:14 +0000;
  • 6f7b330 (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 15:06:14 +0000;
  • a40ef90 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 15:57:24 +0000;
  • e86d2df (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 15:57:24 +0000;
  • 0449660 Added the option plot to complexity.entropy() to suppress plotting of the histogram. by huklein <hansulrich.klein.com> 2021-06-21 23:41:06 -0400;
  • dcd8d58 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 15:46:41 +0000;
  • 02482b8 (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 15:46:40 +0000;
  • 6e7bc2f 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 10:39:28 -0400;
  • 4524058 (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 10:39:28 -0400;
  • 5c24d04 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 18:23:29 +0000;
  • 6bd5837 (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 18:23:29 +0000;
  • d8fd3ed 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 13:35:20 -0400;
  • e9bb707 (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 13:08:18 -0400;
  • 62d3900 Updated readSFF.c to remove warning message during R check. by huklein <hansulrich.klein.com> 2019-10-09 12:09:32 -0400;
  • 458e031 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 12:11:00 -0400;
  • d7102b3 (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 11:53:19 -0400;
  • d61b97b bump x.y.z versions to odd y after creation of RELEASE_3_8 branch by vobencha <vobencha@gmail.com> 2018-10-30 11:54:29 -0400;
  • c3e31d8 (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 11:41:46 -0400;
  • fc463e1 bump x.y.z versions to odd y after creation of RELEASE_3_7 branch by vobencha <valerie.obenchain@roswellpark.org> 2018-04-30 10:41:38 -0400;
  • 4c59153 (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 10:35:15 -0400;
  • bf25816 no more "append" method to import from the Biostrings package by Hervé Pagès <hpages@fredhutch.org> 2018-01-21 17:44:41 -0800;
  • 56beb47 follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12 by Hervé Pagès <hpages@fredhutch.org> 2018-01-21 17:18:23 -0800;
  • 5939f48 (origin/RELEASE_3_6, RELEASE_3_6) Replaced RangedData by GRanges by huklein <hansulrich.klein.com> 2017-12-13 20:55:16 -0500;
  • 539c22e Replaced RangedData by GRanges by huklein <hansulrich.klein.com> 2017-12-13 20:55:16 -0500;
  • 2468448 bump x.y.z versions to odd y after creation of RELEASE_3_6 branch by Hervé Pagès <hpages@fredhutch.org> 2017-10-30 12:52:10 -0400;
  • 31321c2 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 12:39:31 -0400;
  • 46d95e5 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;
  • ef754ed (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;
  • 218e777 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;
  • 124b822 Updated breakpoints.RData. by H-U Klein <h.klein@uni-muenster.de> 2017-04-08 20:51:55 +0000;
  • e691ba6 Updated breakpoints.RData by H-U Klein <h.klein@uni-muenster.de> 2017-04-08 20:51:25 +0000;
  • 97bbac5 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;
  • 2ea5965 (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;
  • 82f6fd7 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;
  • 7c9a7bc Updated documentation and namespace. by H-U Klein <h.klein@uni-muenster.de> 2016-10-10 01:18:30 +0000;
  • d843d25 bump version after creating 3.3 branch by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-03 21:30:44 +0000;
  • d3b4dfa (origin/RELEASE_3_3, RELEASE_3_3) Creating branch for BioC 3.3 release. by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-03 21:26:31 +0000;
  • 97df509 Bump versions prior to creation of 3.3 branch by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-03 21:20:18 +0000;
  • 4b5b8f4 elementLengths was renamed -> elementNROWS in S4Vectors (new name reflects TRUE semantic, old name will be deprecated soon) by Herve Pages <hpages@fhcrc.org> 2016-01-29 01:22:03 +0000;
  • 0b69f23 Adapted ava2vcf() to changes in the underlying VCF class. by H-U Klein <h.klein@uni-muenster.de> 2016-01-11 22:44:57 +0000;
  • 4182be8 Bumped version number of all packages after creation of 3.2 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-10-13 19:59:53 +0000;
  • f2d2771 (origin/RELEASE_3_2, RELEASE_3_2) Creating branch for BioC 3.2 release. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-10-13 19:57:33 +0000;
  • bc7effb Bumped versions of all packages prior to creating 3.2 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-10-13 19:36:05 +0000;
  • 4ccdb17 Some tweaks in response to the SummarizedExperiment class defined in the GenomicRanges package being replaced with the RangedSummarizedExperiment class defined in the new SummarizedExperiment package: - Imports the new SummarizedExperiment package. - Replace all occurences of rowData and exptData with rowRanges and metadata, respectively. - Bump version. by Herve Pages <hpages@fhcrc.org> 2015-05-19 22:32:35 +0000;
  • c46739a Use positive gap penalties for consistency with new Biostrings and msa convention. by Herve Pages <hpages@fhcrc.org> 2015-04-16 22:00:42 +0000;
  • 2fa6f2b (origin/RELEASE_3_1, RELEASE_3_1) Use positive gap penalties for consistency with new Biostrings and msa convention. by Herve Pages <hpages@fhcrc.org> 2015-04-16 21:58:14 +0000;
  • f35229e Bump versions in trunk after creation of 3.1 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-04-16 20:02:44 +0000;
  • 67f4a09 Creating branch for BioC 3.1 release. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-04-16 20:00:01 +0000;
  • 91e128f Bump versions prior to creating 3.1 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-04-16 19:42:01 +0000;
  • 9eeccc9 fixed S4Vectors imports by H-U Klein <h.klein@uni-muenster.de> 2015-03-31 09:42:44 +0000;
  • 0a151fb fixed namespace issues 2 by H-U Klein <h.klein@uni-muenster.de> 2015-03-27 11:44:51 +0000;
  • ff34074 fixed namespace issues by H-U Klein <h.klein@uni-muenster.de> 2015-03-27 11:03:18 +0000;
  • e5107b4 Update VCF rowData argument to rowRanges by James Hester <jhester@fredhutch.org> 2015-03-26 20:03:28 +0000;
  • 6b78771 remove levels from IRanges imports by Dan Tenenbaum <dtenenba@fhcrc.org> 2014-11-26 21:04:51 +0000;
  • b6194c2 Bumping versions after creating 3.0 release branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2014-10-13 21:47:41 +0000;
  • 281c03d (origin/RELEASE_3_0) Creating branch for BioC 3.0 release. by Dan Tenenbaum <dtenenba@fhcrc.org> 2014-10-13 21:46:02 +0000;
  • 036aa73 Bump package versions prior to creating the 3.0 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2014-10-13 21:38:33 +0000;
  • 9f78119 Replaced deprecated countIndex() by elementLengths(). Updated documentation. by H-U Klein <h.klein@uni-muenster.de> 2014-09-30 19:04:49 +0000;
  • 003d309 Updated package description. by H-U Klein <h.klein@uni-muenster.de> 2014-09-30 18:56:49 +0000;
  • 745eda2 Second version bump after creating 2.14 release branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2014-04-11 21:21:21 +0000;
  • 8e76864 (origin/RELEASE_2_14, RELEASE_2_14) Creating 2.14 release branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2014-04-11 21:17:46 +0000;
  • bb3fc4d First version bump prior to creating 2.14 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2014-04-11 21:07:21 +0000;
  • cd612da Modified NAMESPACE to avoid warning when importing graphics::boxplot. by H-U Klein <h.klein@uni-muenster.de> 2014-03-14 14:28:50 +0000;
  • 7d64fd5 modify to new biocViews to DESCRIPTION file by Sonali Arora <sarora@fhcrc.org> 2014-03-04 22:12:21 +0000;
  • 1ed757c Moved package TeachingDemos to Imports by H-U Klein <h.klein@uni-muenster.de> 2013-12-06 11:40:15 +0000;
  • 37eaf3c Removed some packages from Imports by H-U Klein <h.klein@uni-muenster.de> 2013-12-06 10:24:13 +0000;
  • d7ca6cf bug fix in ava2vcf.R by H-U Klein <h.klein@uni-muenster.de> 2013-12-05 21:59:00 +0000;
  • 8b35e0b added vcf example to vignette and minor bug fixes by H-U Klein <h.klein@uni-muenster.de> 2013-12-05 19:54:52 +0000;
  • 01df1b4 bump version after release branch has been created by Dan Tenenbaum <dtenenba@fhcrc.org> 2013-10-14 21:47:19 +0000;
  • 54c33f3 (origin/RELEASE_2_13, RELEASE_2_13) Creating branch for BioC 2.13 release. by Dan Tenenbaum <dtenenba@fhcrc.org> 2013-10-14 21:43:43 +0000;
  • 9744ee7 bump versions prior to creating BioC 2.13 branch by Dan Tenenbaum <dtenenba@fhcrc.org> 2013-10-14 21:29:21 +0000;
  • 93b7fb0 Modified vignette code due to changes in rtracklayer by H-U Klein <h.klein@uni-muenster.de> 2013-10-13 16:28:23 +0000;
  • 2deb385 dapted htmlReport() and the vignette to avoid usage of deprecated methods. by H-U Klein <h.klein@uni-muenster.de> 2013-08-29 15:07:32 +0000;
  • bc37236 Fix breakpoints dataset. Was containing PairwiseAlignedFixedSubject instances, but this class is now defunct in Biostrings (after a 6-month deprecation cycle) and has been replaced by PairwiseAlignmentsSingleSubject. by Herve Pages <hpages@fhcrc.org> 2013-07-12 23:06:06 +0000;
  • 6cb3d46 Use PairwiseAlignments instead of PairwiseAlignedXStringSet class (removed from Biostrings 2.29.2). by Herve Pages <hpages@fhcrc.org> 2013-05-13 22:14:30 +0000;
  • f4c46fc Need to import new XVector package. by Herve Pages <hpages@fhcrc.org> 2013-05-12 20:57:47 +0000;
  • cb843ab Bump y in version x.y.z to odd number in devel by Dan Tenenbaum <dtenenba@fhcrc.org> 2013-04-03 22:06:11 +0000;
  • 4056be3 (origin/RELEASE_2_12, RELEASE_2_12) Creating branch for BioC 2.12 release. by Dan Tenenbaum <dtenenba@fhcrc.org> 2013-04-03 21:56:22 +0000;
  • 93f757f bump y of x.y.z version number for BioC 2.12 release by Dan Tenenbaum <dtenenba@fhcrc.org> 2013-04-03 21:32:27 +0000;
  • 22b0d1a Substituted "%in%" by overlapsAny for RangedData. by H-U Klein <h.klein@uni-muenster.de> 2013-03-11 14:20:54 +0000;
  • 1275019 replace deprecated .find.packages() with find.packages() by Dan Tenenbaum <dtenenba@fhcrc.org> 2013-03-04 17:49:21 +0000;
  • 265a628 (origin/RELEASE_2_11, RELEASE_2_11) merged -r73012:73013 from trunk by H-U Klein <h.klein@uni-muenster.de> 2013-01-30 12:51:26 +0000;
  • f624fc7 merged -r73012:73013 from trunk by H-U Klein <h.klein@uni-muenster.de> 2013-01-30 11:39:40 +0000;
  • 68a5b88 Fixed bug in AVA variant import concerning single base pair deletions by H-U Klein <h.klein@uni-muenster.de> 2013-01-30 11:24:49 +0000;
  • 38b8a49 added SFF examples to vignette by H-U Klein <h.klein@uni-muenster.de> 2013-01-08 14:24:10 +0000;
  • 3e7f4b5 added function to create quality report by H-U Klein <h.klein@uni-muenster.de> 2013-01-08 11:01:00 +0000;
  • b53ba3e added example.sff file by H-U Klein <h.klein@uni-muenster.de> 2013-01-07 11:06:50 +0000;
  • 2a31ba6 added subsetting by H-U Klein <h.klein@uni-muenster.de> 2013-01-06 18:02:50 +0000;
  • 5dc30cb corrected overlong file path by H-U Klein <h.klein@uni-muenster.de> 2013-01-06 18:00:06 +0000;
  • 5f491bc added writeSFF method by H-U Klein <h.klein@uni-muenster.de> 2013-01-06 17:58:42 +0000;
  • f358def corrected overlong file path: by H-U Klein <h.klein@uni-muenster.de> 2013-01-06 17:57:47 +0000;
  • 7a7bcae corrected overlong file path e, and those below, will be ignored-- by H-U Klein <h.klein@uni-muenster.de> 2013-01-06 17:56:20 +0000;
  • eb8bcb4 initial commit by H-U Klein <h.klein@uni-muenster.de> 2013-01-06 17:54:37 +0000;
  • d366d32 initial commit by H-U Klein <h.klein@uni-muenster.de> 2013-01-06 17:54:18 +0000;
  • 31b12bd changed methods import, added writeSFF by H-U Klein <h.klein@uni-muenster.de> 2013-01-06 17:53:31 +0000;
  • db60736 @<- has been moved from methods to base, so it no longer needs to be imported in package NAMESPACEs. by Dan Tenenbaum <dtenenba@fhcrc.org> 2013-01-04 21:18:09 +0000;