1. BiSeq
  2. Graph
Graph of BiSeq
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • | *
  • * |
  • * |
  • |/
  • *
  • *
  • *
  • *
  • *
  • | *
  • |/
  • *
  • *
  • | *
  • |/
  • *
  • *
  • *
  • | *
  • |/
  • *
  • *
  • *
  • | *
  • |/
  • *
  • *
  • *
  • *
  • *
  • | *
  • |/
  • *
  • *
  • *
  • *
  • *
  • *
  • | *
  • |/
  • *
  • *
  • *
  • *
  • *
  • | *
  • * |
  • | *
  • * |
  • * |
  • * |
  • * |
  • | *
  • |/
  • *
  • *
  • *
  • *
  • | *
  • * |
  • * |
  • * |
  • * |
  • * |
  • | *
  • * |
  • * |
  • * |
  • * |
  • | *
  • * |
  • | *
  • * |
  • | *
  • * |
  • * |
  • | *
  • * |
  • * |
  • * |
  • 7386b4e (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 10:26:59 -0400;
  • 9e686d0 (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 10:26:59 -0400;
  • a5c3cc0 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 11:08:12 -0400;
  • 2291602 (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 11:08:12 -0400;
  • 6c8a56c 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 15:14:44 +0000;
  • b5cd494 (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 15:14:44 +0000;
  • 5773d7c Pass serialized S4 instances thru updateObject() by Hervé Pagès <hpages.on.github@gmail.com> 2022-01-14 11:43:32 -0500;
  • 88afd2b Starting with BioC 3.15 + R 4.2, 32-bit Windows is no longer supported so Windows builds are single arch only (i.e. 64-bit only) by Hervé Pagès <hpages.on.github@gmail.com> 2021-12-16 13:23:22 -0800;
  • 167cfff 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 16:07:58 +0000;
  • 5d4449a (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 16:07:58 +0000;
  • 77e44cc 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 15:58:45 +0000;
  • d5b9175 (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 15:58:45 +0000;
  • 810f267 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 10:50:37 -0400;
  • e946e2d (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 10:50:37 -0400;
  • 6155da2 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 18:34:25 +0000;
  • ffaf670 (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 18:34:25 +0000;
  • 6631c66 Undeprecate. by lshep <lori.shepherd@roswellpark.org> 2020-03-31 17:06:41 -0400;
  • f33f5f1 Version. by Katja Hebestreit <katja.hebestreit@gmail.com> 2020-03-27 17:27:12 -0700;
  • e45dd98 Fixed argument naming. by Katja Hebestreit <katja.hebestreit@gmail.com> 2020-03-27 17:26:48 -0700;
  • 6aeb20c Fixed BSraw class check. by Katja Hebestreit <katja.hebestreit@gmail.com> 2020-03-27 17:26:21 -0700;
  • 6c6778c Updated email address. by Katja Hebestreit <katja.hebestreit@gmail.com> 2020-03-23 15:46:01 -0700;
  • b7b66c3 Deprecation package by lshep <lori.shepherd@roswellpark.org> 2020-01-06 10:50:33 -0500;
  • 9995427 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 13:36:50 -0400;
  • 1e02352 (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 13:08:39 -0400;
  • 6d795db 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 12:11:22 -0400;
  • 6338250 (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 11:53:42 -0400;
  • 0c59006 bump x.y.z versions to odd y after creation of RELEASE_3_8 branch by vobencha <vobencha@gmail.com> 2018-10-30 11:54:31 -0400;
  • ca0eb05 (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 11:41:51 -0400;
  • a9c69e6 (origin/RELEASE_3_7, RELEASE_3_7) update old serialized BSraw instance by Hervé Pagès <hpages@fredhutch.org> 2018-04-30 12:29:05 -0700;
  • d746240 update old serialized BSraw instance by Hervé Pagès <hpages@fredhutch.org> 2018-04-30 12:29:05 -0700;
  • 09de32a bump x.y.z versions to odd y after creation of RELEASE_3_7 branch by vobencha <valerie.obenchain@roswellpark.org> 2018-04-30 10:41:39 -0400;
  • b833dc8 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 10:35:30 -0400;
  • be9fc40 bump x.y.z versions to odd y after creation of RELEASE_3_6 branch by Hervé Pagès <hpages@fredhutch.org> 2017-10-30 12:52:48 -0400;
  • b595dc0 (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 12:40:02 -0400;
  • a4bc57d 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;
  • 47ad6c1 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;
  • 3359e6b (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;
  • db35abe 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;
  • 9393e0b 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;
  • 8675f57 (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;
  • 8fd5f9c 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;
  • e3fd2c2 mark as unsupported on win32 until Windows binary of lokern package (which BiSeq relies on) gets fixed on CRAN (doesn't contain i386 DLL right now) by Herve Pages <hpages@fhcrc.org> 2016-10-09 21:30:35 +0000;
  • a60f122 bump version after creating 3.3 branch by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-03 21:30:44 +0000;
  • ef6faa5 (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;
  • e5218de Bump versions prior to creation of 3.3 branch by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-03 21:20:18 +0000;
  • d6859a9 use accessors instead of direct slot access on Hits objects by Herve Pages <hpages@fhcrc.org> 2016-02-22 10:35:36 +0000;
  • 8845dd5 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;
  • f2cb51a (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;
  • 7e7d851 Bumped versions of all packages prior to creating 3.2 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-10-13 19:36:05 +0000;
  • fbe51a5 Fix BSraw() and BSrel() constructor functions by making them agnostic of the internals of parent class RangedSummarizedExperiment. This should prevent them from breaking again next time RangedSummarizedExperiment internals change (not that we plan to change them again anytime soon though). by Herve Pages <hpages@fhcrc.org> 2015-06-22 06:06:20 +0000;
  • cf4ff75 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 23:15:56 +0000;
  • 92d5921 - BSrel and BSraw classes now extend new RangedSummarizedExperiment class from SummarizedExperiment package instead of "old" SummarizedExperiment class from GenomicRanges package. - Update serialized BSrel and BSraw objects contained in the package. by Herve Pages <hpages@fhcrc.org> 2015-05-11 22:08:40 +0000;
  • eb1bd86 Bump versions in trunk after creation of 3.1 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-04-16 20:02:44 +0000;
  • 79912f2 (origin/RELEASE_3_1, RELEASE_3_1) Creating branch for BioC 3.1 release. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-04-16 20:00:01 +0000;
  • 28043f2 Bump versions prior to creating 3.1 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-04-16 19:42:01 +0000;
  • 6700e03 One correction in the vignette. by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2015-04-02 02:05:25 +0000;
  • e218032 Updated the vignette. by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2015-04-01 00:07:03 +0000;
  • e7b3f9a Various fixes: - Fix calls to new("BSraw", ...) and new("BSrel", ...) (the 'rowData' slot has not been renamed 'rowRanges' yet in the definition of parent class SummarizedExperiment). - Use mcols() instead of elementMetadata() (they're equivalent but the former is the recommended one). - Import the GenomeInfoDb package (the seqlevels getter and setter are used internally). - Use :: instead of ::: in IRanges::width by Herve Pages <hpages@fhcrc.org> 2015-03-24 20:33:09 +0000;
  • 672dd21 Changed all 'rowData' to 'rowRanges' for new version of GenomicRanges classes. by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2015-03-24 03:01:20 +0000;
  • c7209e7 Bumping versions after creating 3.0 release branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2014-10-13 21:47:41 +0000;
  • ae87c28 (origin/RELEASE_3_0) Creating branch for BioC 3.0 release. by Dan Tenenbaum <dtenenba@fhcrc.org> 2014-10-13 21:46:02 +0000;
  • bb993be Bump package versions prior to creating the 3.0 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2014-10-13 21:38:33 +0000;
  • 22b9750 need to import S4Vectors by Herve Pages <hpages@fhcrc.org> 2014-07-23 18:21:12 +0000;
  • 87593eb emoved a warning caused by not using the full name of a data.frame columns in summerizeRegions(). by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2014-07-22 03:35:49 +0000;
  • 5a228bc It is now possible to set the maximum distance for the variogram. Makes it a lot faster. by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2014-06-27 00:13:34 +0000;
  • 6f06b3b The variogram can now be estimated for a subset of the clusters only. Makes it a lot faster. by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2014-06-25 06:31:53 +0000;
  • c478e5d (origin/RELEASE_2_14, RELEASE_2_14) clarified readBismark manual. by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2014-05-06 21:34:28 +0000;
  • 4263562 clarified readBismark manual. by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2014-05-06 21:31:15 +0000;
  • 9ab9fc7 clusterSites throws a more meaningful error when there are no CpG clusters in the data. by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2014-04-22 18:54:52 +0000;
  • ece4235 cluster.sites throws a more meaningful error when there are no CpG clusters found. by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2014-04-21 21:27:55 +0000;
  • 9d750db Small bug in the manual. by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2014-04-18 23:30:12 +0000;
  • 8b86892 Updated manuals and email address. by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2014-04-18 23:20:48 +0000;
  • 58de4ce Second version bump after creating 2.14 release branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2014-04-11 21:21:21 +0000;
  • d6da995 Creating 2.14 release branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2014-04-11 21:17:46 +0000;
  • 1c9a018 First version bump prior to creating 2.14 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2014-04-11 21:07:21 +0000;
  • 6d8897c Removed a small bug in the trimClusters method. by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2014-03-13 23:47:54 +0000;
  • 62e5ce8 Pointed out in the man pages that compressed files can be used for readBismark(). by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2014-03-13 17:31:58 +0000;
  • 20b2641 Files which are read by readBismark are allowed to have headers beginning with a '#' now. by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2014-03-11 18:05:17 +0000;
  • ff34f49 (origin/RELEASE_2_13, RELEASE_2_13) readBismark manual adapted to new Bismark version. by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2014-03-05 01:12:18 +0000;
  • 363ddb3 readBismark manual adapted to new Bismark version. by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2014-03-05 01:10:03 +0000;
  • 50db93a modify biocViews to remove duplicated biocViews by Sonali Arora <sarora@fhcrc.org> 2014-03-04 23:47:10 +0000;
  • 5ec6736 modify to new biocViews to DESCRIPTION file by Sonali Arora <sarora@fhcrc.org> 2014-03-04 22:12:21 +0000;
  • 633af7c Model is checked for convergence. If not converged, results are set to NA. by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2014-02-20 02:06:44 +0000;
  • 1cc4140 Updated Description file by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2014-02-05 14:22:42 +0000;
  • 194be9d Fixed bug in readBismark() by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2014-02-05 14:21:31 +0000;
  • 5157fce Fixed bug in readBismark() -This line, and those below, will be ignored-- by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2014-02-05 14:14:16 +0000;
  • 404a785 Small bug fixed. by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2013-12-10 10:47:34 +0000;
  • 5948bf1 New splitting approach for a faster run, if parallelized. by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2013-11-28 12:54:48 +0000;
  • e45042a writeBED() was updated due to changes in rtracklayer package by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2013-11-25 10:42:47 +0000;
  • c42aa32 can handle CompressedCharacterList in elementMetadata column by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2013-11-20 18:40:21 +0000;
  • 6df6e40 can handle CompressedCharacterList in elementMetadata column by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2013-11-20 18:39:58 +0000;
  • 59e0f0c version number by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2013-11-20 16:07:38 +0000;
  • fb881bd version number by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2013-11-20 16:06:07 +0000;
  • 7023234 identifier ids occur only once per annotated ranges by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2013-11-20 15:59:39 +0000;
  • ad9970e identifier ids occure only once per annotated ranges by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2013-11-20 15:59:07 +0000;
  • 6abf70f rename inst/doc to vignettes and bump version by Dan Tenenbaum <dtenenba@fhcrc.org> 2013-11-01 20:30:03 +0000;
  • 8338db7 z-scores that are -Inf or Inf are set to NA by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2013-10-31 11:15:35 +0000;
  • 8f2e550 Version number by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2013-10-31 11:05:11 +0000;
  • d599a27 z-scores that are -Inf or Inf are set to NA M makeVariogram.R by Katja Hebestreit <katja.hebestreit@uni-muenster.de> 2013-10-31 10:38:54 +0000;
  • 1f8ba35 bump version after release branch has been created by Dan Tenenbaum <dtenenba@fhcrc.org> 2013-10-14 21:47:19 +0000;