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  • 4cb69fb (HEAD -> master, origin/master, origin/HEAD) 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 15:21:13 +0000;
  • 2a0b33e (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 15:21:13 +0000;
  • 04a381f updated_description by Kamal Kishore <kishor01@c02fx59jmd6r.broadband> 2022-03-15 18:17:03 +0000;
  • e4194ac clusterapply by Kamal Kishore <kishor01@c02fx59jmd6r.cri.camres.org> 2022-03-14 13:19:15 +0000;
  • 9aa5834 Pass serialized S4 instances thru updateObject() by Hervé Pagès <hpages.on.github@gmail.com> 2021-11-21 00:33:15 -0500;
  • 518a53e Deprecation by lshep <lori.shepherd@roswellpark.org> 2021-11-15 13:35:48 -0500;
  • e1a42e2 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 16:15:34 +0000;
  • 34972d4 (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 16:15:34 +0000;
  • bc4d8d8 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 16:07:06 +0000;
  • ca8dade (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 16:07:06 +0000;
  • c23dd2d 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 10:58:28 -0400;
  • 5afa573 (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 10:58:28 -0400;
  • 830e7ba fixed plotMeth function by kamalfartiyal84 <kamal.fartiyal84@gmail.com> 2020-10-19 11:58:00 +0100;
  • 981fb68 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 18:42:39 +0000;
  • 403df4a (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 18:42:39 +0000;
  • a63ba46 setenv error fix by kamalfartiyal84 <kamal.fartiyal84@gmail.com> 2020-03-11 15:50:16 +0000;
  • 7d5087a 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 13:37:59 -0400;
  • b631764 (origin/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 13:09:03 -0400;
  • 2f6cd9d 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 12:11:42 -0400;
  • 72edb06 (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 11:53:49 -0400;
  • 07b5435 cposdensity by kamalfartiyal84 <kamal.fartiyal84@gmail.com> 2019-03-07 16:25:39 +0000;
  • 37cf44b news by kamalfartiyal84 <kamal.fartiyal84@gmail.com> 2019-03-07 16:25:22 +0000;
  • 50f6409 description by kamalfartiyal84 <kamal.fartiyal84@gmail.com> 2019-03-07 16:25:12 +0000;
  • 8fd1847 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;
  • 0cc3f02 (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 11:41:55 -0400;
  • 77b0b3e 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;
  • 9b65a0b (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;
  • 424e2a5 bump x.y.z versions to odd y after creation of RELEASE_3_6 branch by Hervé Pagès <hpages@fredhutch.org> 2017-10-30 12:53:37 -0400;
  • 76c3ebf (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 12:40:27 -0400;
  • f031813 Bump version of packages that define RangedSummarizedExperiment derivatives (direct or indirect). Will help get rid of those class definitions that are cached on the user machines and became stale after GenomicRangesORGRangesList was renamed GenomicRanges_OR_GRangesList (on June 18, commit 130486). by Herve Pages <hpages@fhcrc.org> 2017-06-27 17:05:27 +0000;
  • ce2f0b4 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;
  • 1436c60 (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;
  • 403b1ce 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;
  • cd0fcc5 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;
  • 93d8cf1 (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;
  • 93367cb 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;
  • 9996979 (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;
  • e23a158 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;
  • 570258c 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;
  • 55f33e0 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;
  • 0d300c0 bump version after creating 3.3 branch by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-03 21:30:44 +0000;
  • 65bd807 Creating branch for BioC 3.3 release. by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-03 21:26:31 +0000;
  • 743ab8e Bump versions prior to creation of 3.3 branch by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-03 21:20:18 +0000;
  • ffe87f0 (origin/RELEASE_3_2, RELEASE_3_2) Fixed pool.reads by Kamal Kishore <kamal.fartiyal84@gmail.com> 2016-03-16 15:50:48 +0000;
  • 409e493 Fixed pool.reads by Kamal Kishore <kamal.fartiyal84@gmail.com> 2016-03-16 15:49:12 +0000;
  • 2c5c974 Updated pool.reads by Kamal Kishore <kamal.fartiyal84@gmail.com> 2016-03-16 09:32:13 +0000;
  • a51e1ea Updated profileDNAmetBin by Kamal Kishore <kamal.fartiyal84@gmail.com> 2016-03-02 08:28:56 +0000;
  • 294dc2a Updated description by Kamal Kishore <kamal.fartiyal84@gmail.com> 2016-03-01 11:15:02 +0000;
  • bfa83bc Updated profileDNAmetBin by Kamal Kishore <kamal.fartiyal84@gmail.com> 2016-02-29 08:03:46 +0000;
  • 603aed6 updated description by Kamal Kishore <kamal.fartiyal84@gmail.com> 2016-02-24 11:35:04 +0000;
  • 0a12988 Updated profileDNAmetBin by Kamal Kishore <kamal.fartiyal84@gmail.com> 2016-02-24 11:31:26 +0000;
  • b0ae0c4 Updated devel version by Kamal Kishore <kamal.fartiyal84@gmail.com> 2016-01-25 16:29:03 +0000;
  • 092bc54 Updated methstats by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-11-24 17:05:33 +0000;
  • b142a09 Updated man pages of BSprepare, findDMR and meth.call by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-11-24 16:06:03 +0000;
  • 7b89801 Updated meth.call by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-11-24 11:04:03 +0000;
  • d36b4fe Updated findDMR by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-11-17 16:13:00 +0000;
  • 6517dbe Updated methstats function by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-11-10 13:41:08 +0000;
  • d36118a Added pool.reads by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-11-04 11:39:31 +0000;
  • e1185a2 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;
  • a49a5e0 Creating branch for BioC 3.2 release. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-10-13 19:57:33 +0000;
  • fcffaea Bumped versions of all packages prior to creating 3.2 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-10-13 19:36:05 +0000;
  • 668989e (origin/RELEASE_3_1, RELEASE_3_1) updated description by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-09-29 09:46:22 +0000;
  • 0de7c50 Added citation by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-09-29 09:45:01 +0000;
  • a65a8d6 Added paper CITATION by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-09-29 09:42:42 +0000;
  • dcdc86f Updated meth.call function coverage method with anamoly noticed in Athaliana by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-09-17 13:14:02 +0000;
  • 1912cf9 Updated description by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-09-17 13:10:17 +0000;
  • f312ff2 Updated meth.call function with the coverage function anamoly encountered in Athaliana by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-09-17 13:09:22 +0000;
  • 814d2dc Re-serialize (again) RangedSummarizedExperiment objects included in the package in response to latest changes in RangedSummarizedExperiment internals. by Herve Pages <hpages@fhcrc.org> 2015-06-18 23:21:03 +0000;
  • c18655c description updated by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-06-08 13:46:11 +0000;
  • 8df3157 NEWS updated by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-06-08 12:54:18 +0000;
  • 49359a9 updated profileDNAmetBinParallel by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-05-19 16:16:49 +0000;
  • 6e7fe5f fixed profileDNAmetBinParallel by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-05-19 16:02:02 +0000;
  • b613328 Update serialized GEcollection objects (inst/extdata/gec.H1.Rdata and inst/extdata/gec.IMR90.Rdata) included in the package. by Herve Pages <hpages@fhcrc.org> 2015-05-13 00:47:39 +0000;
  • 8c81933 GEcollection class now extends new RangedSummarizedExperiment class from SummarizedExperiment package instead of "old" SummarizedExperiment class from GenomicRanges package. by Herve Pages <hpages@fhcrc.org> 2015-05-11 22:57:14 +0000;
  • cd3de1c Updated getCposchr by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-05-11 09:04:18 +0000;
  • cf739d8 Fixed cytosine counting bug by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-05-08 15:21:45 +0000;
  • bdcbee1 Fixed cytosine counting related bug by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-05-08 15:18:13 +0000;
  • c46bee6 Updated coverage information in findDMR and meth.call by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-05-08 10:34:25 +0000;
  • 26fbb10 Updated coverage information in meth.call & findDMRs by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-05-08 10:06:51 +0000;
  • 1dd7b0d Updating the development version same as release branch by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-04-27 13:50:28 +0000;
  • 883597d fixed rowRanges instead of rowData by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-04-27 09:26:01 +0000;
  • e864c64 Updated vignette for plotMeth example by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-04-22 11:16:53 +0000;
  • 7876d11 Fixed bug in Significance argument of mapBSdata2GRanges by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-04-21 14:09:23 +0000;
  • 5da6fc0 Updated plotMeth by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-04-21 10:13:02 +0000;
  • c57ab2d Updated plotMeth function by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-04-20 16:53:30 +0000;
  • 9250ebc Bump versions in trunk after creation of 3.1 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-04-16 20:02:44 +0000;
  • a058c5c Creating branch for BioC 3.1 release. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-04-16 20:00:01 +0000;
  • 455189d Bump versions prior to creating 3.1 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-04-16 19:42:01 +0000;
  • 688635c Replaced rowData with rowRanges by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-03-30 09:54:09 +0000;
  • 3494a2f (origin/RELEASE_3_0) removed unneccesary files by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-03-30 09:37:38 +0000;
  • 08d1e90 removed unnecessary files by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-03-30 09:35:54 +0000;
  • a845630 Updated development version according to release version by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-03-30 09:32:48 +0000;
  • 29f835f need to import BSgenome (+ some other tweaks to NAMESPACE) by Herve Pages <hpages@fhcrc.org> 2015-03-19 22:47:26 +0000;
  • c9528a1 Updated dates and version by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-02-25 09:33:53 +0000;
  • 4a251fa updated BSdataSet by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-02-24 16:49:58 +0000;
  • b1467fd Updated dates by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-02-24 14:22:20 +0000;
  • 3adeb21 updated NAMEspace by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-02-24 10:18:28 +0000;
  • 20701bf updated methstats by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-02-24 09:45:38 +0000;
  • 1357063 added extdata files with updated tabix index by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-02-23 17:09:27 +0000;
  • 80edff0 Updates BSprepare, examples and vignette by Kamal Kishore <kamal.fartiyal84@gmail.com> 2015-02-23 17:06:41 +0000;