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  • e8e7100 (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 09:42:05 -0400;
  • 404c5e4 (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 09:42:05 -0400;
  • 6ef74a5 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 10:39:25 -0400;
  • b512cbe (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 10:39:25 -0400;
  • 551df97 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 14:57:10 +0000;
  • 0fe801c (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 14:57:10 +0000;
  • e64ddb1 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 15:48:11 +0000;
  • 55210d8 (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 15:48:11 +0000;
  • 0a1b891 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 15:35:55 +0000;
  • 5a966e0 (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 15:35:55 +0000;
  • 4567bd5 version bump by LiNk-NY <mramos09@gmail.com> 2021-01-25 13:51:40 -0500;
  • 43267f9 replace old Sexpr with new code by LiNk-NY <mramos09@gmail.com> 2021-01-25 13:51:38 -0500;
  • bda4776 version bump by LiNk-NY <mramos09@gmail.com> 2021-01-13 09:14:24 -0500;
  • 87365ba Merge pull request <a href="#2">#2</a> from Bioconductor/keggrest by Marcel Ramos <LiNk-NY@users.noreply.github.com> 2021-01-13 09:13:22 -0500;
  • 70aed96 update code to use KEGGREST by LiNk-NY <mramos09@gmail.com> 2021-01-12 16:21:07 -0500;
  • c467513 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 10:26:14 -0400;
  • ad478ca (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 10:26:14 -0400;
  • de14c93 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 18:11:31 +0000;
  • 3368428 (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 18:11:31 +0000;
  • 71e3a7a (origin/RELEASE_3_10, RELEASE_3_10) Fix to ChromBand vignette to use karyotypeR instead of SNPchip which was deprecated. by Jim MacDonald <jmacdon@ogopogo.deohs.washington.edu> 2019-11-08 09:20:13 -0800;
  • 3833865 Merge branch 'rcastelo-FixChromBand' by Jim MacDonald <jmacdon@ogopogo.deohs.washington.edu> 2019-11-08 09:20:13 -0800;
  • 88d9da7 Fix the vignette ChromBand by replacing the use of the deprecated package SNPchip by karyoploteR. by [rcastelo] <[robert.castelo@upf.edu]> 2019-11-08 17:01:35 +0100;
  • ab8abe0 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 13:34:39 -0400;
  • d211ed7 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 13:07:33 -0400;
  • e406871 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 12:10:39 -0400;
  • d96f0b2 (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 11:53:04 -0400;
  • 941819a (origin/RELEASE_3_8, RELEASE_3_8) Bugfix to allow GO hypergeometric testing with NOSCHEMA OrgDb packages. by Jim MacDonald <jmacdon@ogopogo.deohs.washington.edu> 2019-03-07 12:22:20 -0800;
  • b847a88 Bugfix to allow GO hypergeometric using OrgDb of NOSCHEMA persuasion. by Jim MacDonald <jmacdon@ogopogo.deohs.washington.edu> 2019-03-07 12:18:45 -0800;
  • 9817aa1 bump x.y.z versions to odd y after creation of RELEASE_3_8 branch by vobencha <vobencha@gmail.com> 2018-10-30 11:54:26 -0400;
  • 17461d5 bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch by vobencha <vobencha@gmail.com> 2018-10-30 11:41:42 -0400;
  • 98f80d1 replace biocLite with BiocManager::install by LiNk-NY <mramos09@gmail.com> 2018-07-18 17:12:36 -0400;
  • c73e0eb bump x.y.z versions to odd y after creation of RELEASE_3_7 branch by vobencha <valerie.obenchain@roswellpark.org> 2018-04-30 10:41:36 -0400;
  • c8aeee4 (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 10:35:02 -0400;
  • f6392bb Changes so OBO and GeneSet objects will still work correctly. by Jim MacDonald <jmacdon@ogopogo.deohs.washington.edu> 2017-11-15 15:50:35 -0800;
  • e2ef3d3 Forgot to add unit tests for the changes in the previous commit. by Jim MacDonald <jmacdon@ogopogo.deohs.washington.edu> 2017-11-08 14:57:13 -0800;
  • 05351fd Modified the pipeline for doing Fisher's exact tests to allow people to use either an installed AnnotationDb package (as per usual) or a downloaded AnnotationDb object, from e.g., AnnotationHub. by Jim MacDonald <jmacdon@ogopogo.deohs.washington.edu> 2017-11-08 14:54:56 -0800;
  • 0eeb500 bump x.y.z versions to odd y after creation of RELEASE_3_6 branch by Hervé Pagès <hpages@fredhutch.org> 2017-10-30 12:52:05 -0400;
  • eaba50c (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 12:39:05 -0400;
  • 1fb2b9c Category / GOstats updates from R. Castelo by Martin Morgan <mtmorgan@fhcrc.org> 2017-08-01 19:43:39 +0000;
  • ab6877e import dbGetQuery() from DBI instead of RSQLite by Valerie Obenchain <vobencha@fhcrc.org> 2017-06-23 19:39:42 +0000;
  • 382c817 (origin/RELEASE_3_5, RELEASE_3_5) import dbGetQuery() from DBI instead of RSQLite by Valerie Obenchain <vobencha@fhcrc.org> 2017-06-23 19:37:57 +0000;
  • b827c7c 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;
  • d7c1398 Creating branch for BioC 3.5 release by Herve Pages <hpages@fhcrc.org> 2017-04-24 19:45:44 +0000;
  • 09f9d24 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;
  • be26db3 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;
  • d4798dc (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;
  • 0d5ec9e 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;
  • 7bc7e83 bump version after creating 3.3 branch by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-03 21:30:44 +0000;
  • bfe6f80 (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;
  • dfa6cd9 Bump versions prior to creation of 3.3 branch by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-03 21:20:18 +0000;
  • 837cf72 cleanup: various by Martin Morgan <mtmorgan@fhcrc.org> 2016-01-13 20:18:50 +0000;
  • 42065c9 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;
  • 2a90401 (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;
  • c9433ec Bumped versions of all packages prior to creating 3.2 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-10-13 19:36:05 +0000;
  • 272a36e (origin/RELEASE_3_1, RELEASE_3_1) Bugfix for previous bugfix... by James MacDonald <jmacdon@med.umich.edu> 2015-05-14 20:07:36 +0000;
  • 5b7f616 Bugfix to .setKeytypes to allow users to do PFAM based hypergeometric using org packages for annotation. by James MacDonald <jmacdon@med.umich.edu> 2015-05-12 15:27:27 +0000;
  • 8ce32e4 Bugfix to .setKeytype to allow for PFAM hypergeometric using Org package as annotation. by James MacDonald <jmacdon@med.umich.edu> 2015-05-12 14:39:20 +0000;
  • 0a886d6 Bump versions in trunk after creation of 3.1 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-04-16 20:02:44 +0000;
  • bdf50ec Creating branch for BioC 3.1 release. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-04-16 20:00:01 +0000;
  • 981b9c6 Bump versions prior to creating 3.1 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-04-16 19:42:01 +0000;
  • 4a90cde Export the "organism" methods. No idea why they were not exported, but the categoryCompare needs that (it uses the method for HyperGParams objects internally). by Herve Pages <hpages@fhcrc.org> 2015-03-18 23:29:40 +0000;
  • 927906f Use the new BiocGenerics::organism() generic for local method definitions instead of annotate::organism() generic (now gone). by Herve Pages <hpages@fhcrc.org> 2015-03-18 22:51:05 +0000;
  • 1914e97 Bumping versions after creating 3.0 release branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2014-10-13 21:47:41 +0000;
  • 34068e3 (origin/RELEASE_3_0) Creating branch for BioC 3.0 release. by Dan Tenenbaum <dtenenba@fhcrc.org> 2014-10-13 21:46:02 +0000;
  • 3b0cca8 Bump package versions prior to creating the 3.0 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2014-10-13 21:38:33 +0000;
  • 148bd8a Updates Category to accomodate PFAM categories for yeast. by Marc Carlson <mcarlson@fhcrc.org> 2014-10-01 23:06:09 +0000;
  • a59aa05 changes to phase out use of defunct PFAM bimaps. by Marc Carlson <mcarlson@fhcrc.org> 2014-09-30 22:34:16 +0000;
  • e73a8bf Some changes to make things work now that PFAM bimaps are defunct. by Marc Carlson <mcarlson@fhcrc.org> 2014-09-30 20:10:09 +0000;
  • 7c484d9 Add dependency on stats4 and import summary() from it. This is an S4 generic and Category defines and exports at least one S4 method for it. by Herve Pages <hpages@fhcrc.org> 2014-09-13 01:12:40 +0000;
  • e08eab6 import the tail() generic from utils by Herve Pages <hpages@fhcrc.org> 2014-05-15 17:57:08 +0000;
  • 5f8660f Second version bump after creating 2.14 release branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2014-04-11 21:21:21 +0000;
  • 351eb8e (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;
  • e381899 First version bump prior to creating 2.14 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2014-04-11 21:07:21 +0000;
  • 02677d1 Rename inst/doc to vignettes and bump version for all packages maintained by BioC core which are in the manifest and have not already done this. by Dan Tenenbaum <dtenenba@fhcrc.org> 2013-10-25 21:19:52 +0000;
  • 35da4bd bump version after release branch has been created by Dan Tenenbaum <dtenenba@fhcrc.org> 2013-10-14 21:47:19 +0000;
  • df61454 (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;
  • cba9e1f bump versions prior to creating BioC 2.13 branch by Dan Tenenbaum <dtenenba@fhcrc.org> 2013-10-14 21:29:21 +0000;
  • 268a0f4 add hyperg function to operate on lists of character vectors by Martin Morgan <mtmorgan@fhcrc.org> 2013-09-14 03:34:05 +0000;
  • 451a253 Example now uses sparse=TRUE by Wolfgang Huber <w.huber@dkfz-heidelberg.de> 2013-06-08 14:35:00 +0000;
  • 5c83869 Added sparse matrix option to cateGOry. by Wolfgang Huber <w.huber@dkfz-heidelberg.de> 2013-06-08 14:32:22 +0000;
  • fd47f42 Fixes a bug caused by an improvement in limma. by Marc Carlson <mcarlson@fhcrc.org> 2013-04-22 22:48:32 +0000;
  • 7b44f76 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;
  • 697fb7e (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;
  • 4f0093b 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;
  • 2a344d1 @<- 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;
  • e7051ce Updates syncs client code with changes to the server. by Marc Carlson <mcarlson@fhcrc.org> 2012-11-27 19:14:04 +0000;
  • e8bf3d6 bump package versions after creating 2.11 branch by Dan Tenenbaum <dtenenba@fhcrc.org> 2012-10-01 22:43:56 +0000;
  • 2c7f7c6 (origin/RELEASE_2_11, RELEASE_2_11) Creating branch for BioC 2.11 release. by Dan Tenenbaum <dtenenba@fhcrc.org> 2012-10-01 22:37:11 +0000;
  • 27130da Bump all packages before creating 2.11 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2012-10-01 22:16:24 +0000;
  • 837da42 The 'annotation' and 'annotation<-' generics have been moved from Biobase (2.17.8) to BiocGenerics (0.3.2). All packages that 'setMethods' on these generics import them from BiocGenerics. by Valerie Obenchain <vobencha@fhcrc.org> 2012-09-18 18:38:46 +0000;
  • b91475a change in the way cytoband dataset is accessed by Dan Tenenbaum <dtenenba@fhcrc.org> 2012-07-11 21:23:15 +0000;
  • a5d238a updated biocViews by Paul Shannon <pshannon@fhcrc.org> 2012-04-27 23:18:55 +0000;
  • f59ce75 Cleanup: o Remove functions made defunct in earlier release o Reactivate unit tests o Remove tests which broke with changing annotation data o Fix partial argument name NOTEs by Dan Tenenbaum <dtenenba@fhcrc.org> 2012-04-20 01:21:30 +0000;
  • 84c076b bumped version numbers after creating 2.10 branch by Dan Tenenbaum <dtenenba@fhcrc.org> 2012-03-30 22:15:56 +0000;
  • 629b17c (origin/RELEASE_2_10, RELEASE_2_10) Creating branch for BioC 2.10 release. by Dan Tenenbaum <dtenenba@fhcrc.org> 2012-03-30 22:10:45 +0000;
  • 24d7414 first version bump prior to creating 2.10 branch by Dan Tenenbaum <dtenenba@fhcrc.org> 2012-03-30 22:05:02 +0000;
  • b66e86f Version bump by Michael Lawrence <lawremi@iastate.edu> 2012-03-29 14:26:17 +0000;
  • fb666ae Fix up documentation for recent changes by Michael Lawrence <lawremi@iastate.edu> 2012-03-29 14:25:56 +0000;
  • e49360b summary,LinearMResult now includes columns for Conditional and TestDirection. This makes it easier to rbind() results from tests with different parameter settings. by Michael Lawrence <lawremi@iastate.edu> 2012-03-29 14:25:38 +0000;
  • 55496cd Fix up my previous work toward generalizing LinearMTest. The initial generalization failed to incorporate the hierarchy in the incidence matrix, where parent terms have the genes of their children. by Michael Lawrence <lawremi@iastate.edu> 2012-03-29 14:24:40 +0000;