Bioconductor Code: TCC

Graph of TCC

8a4c02e (HEAD -> devel, origin/master, origin/devel, origin/HEAD) bump x.y.z version to odd y following creation of RELEASE_3_20 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2024-10-29 09:47:48 -0400;
3ade550 (origin/RELEASE_3_20, RELEASE_3_20) bump x.y.z version to even y prior to creation of RELEASE_3_20 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2024-10-29 09:47:48 -0400;
200654e bump x.y.z version to odd y following creation of RELEASE_3_19 branch by J Wokaty <jwokaty@users.noreply.github.com> 2024-04-30 10:33:13 -0400;
bbe4206 (origin/RELEASE_3_19, RELEASE_3_19) bump x.y.z version to even y prior to creation of RELEASE_3_19 branch by J Wokaty <jwokaty@users.noreply.github.com> 2024-04-30 10:33:13 -0400;
5284308 delete test code related with deprecated functions. by jsun <sun@biunit.dev> 2024-01-09 13:26:02 +0900;
cf0d861 delete bayseq from vignette. by jsun <sun@biunit.dev> 2024-01-04 02:30:35 +0900;
ade83f4 delete bayseq codes in vignette and other script files. by jsun <sun@biunit.dev> 2023-12-12 14:27:54 +0900;
5b13717 changed maintainers e-mail. by jsun <sun@biunit.dev> 2023-11-30 14:44:53 +0900;
36bc857 delete dependencies (bayseq) by jsun <sun@aabbdd.jp> 2023-11-30 14:30:37 +0900;
8063432 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 09:55:38 -0400;
b2650a4 (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 09:55:38 -0400;
96bb7c4 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 10:28:30 -0400;
462af54 (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 10:28:30 -0400;
d0e3c35 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 11:08:38 -0400;
81d0810 (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 11:08:38 -0400;
d1ce08f 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 15:16:05 +0000;
0295ffc (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 15:16:05 +0000;
ff9cdf7 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 16:09:39 +0000;
f3e5d27 (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 16:09:39 +0000;
c4c22b5 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 16:00:26 +0000;
c9bfbb9 (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 16:00:26 +0000;
e0d4132 change exactTest to F-test when edgeR is selected. by jsun <sun@aabbdd.jp> 2021-03-11 19:56:29 +0900;
5ec5b50 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 10:52:27 -0400;
40c62a0 (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 10:52:27 -0400;
f78a725 ressolved merge conflict in DESCRIPTION file. by jsun <wukong@bi.a.u-tokyo.ac.jp> 2020-08-25 15:41:06 +0900;
e599537 delete deseq option since DESeq will be removed from Bioconductor. by jsun <wukong@bi.a.u-tokyo.ac.jp> 2020-08-25 15:35:05 +0900;
8add52c 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 18:36:08 +0000;
61930ac (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 18:36:08 +0000;
619fb61 change if condition for checking class name. by jsun <wukong@bi.a.u-tokyo.ac.jp> 2020-03-23 15:13:13 +0900;
8ad2e93 registered S3 method (plot) that used in TCC. by jsun <j.sun@affrc.go.jp> 2019-12-09 13:16:09 +0900;
9c98620 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 13:36:56 -0400;
1a87441 (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 13:08:46 -0400;
ed21481 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 12:11:26 -0400;
132c4f5 (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 11:53:44 -0400;
e3a874b fixed merge conflict. by jqsun <wukong@bi.a.u-tokyo.ac.jp> 2019-02-09 09:53:40 +0900;
1763a9e changed the function of filterLowCountGenes. by jqsun <wukong@bi.a.u-tokyo.ac.jp> 2019-02-09 09:51:24 +0900;
bb586e8 (origin/RELEASE_3_8, RELEASE_3_8) Add ImmunoOncology biocViews term by Kayla-Morrell <kayla.morrell@roswellpark.org> 2019-01-04 13:18:01 -0500;
48f8edb Add ImmunoOncology biocViews term by Kayla-Morrell <kayla.morrell@roswellpark.org> 2019-01-04 13:17:58 -0500;
652c2c5 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;
56d6e7b bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch by vobencha <vobencha@gmail.com> 2018-10-30 11:41:52 -0400;
92c07bb additional updates from BiocInstaller to BiocManager by LiNk-NY <marcel.ramosperez@roswellpark.org> 2018-09-06 15:53:06 +0000;
0a4c723 changed description of filterLowCountGenes function. by jqsun <wukong@bi.a.u-tokyo.ac.jp> 2018-08-21 17:13:02 +0900;
075b9fe (origin/RELEASE_3_7, RELEASE_3_7) changed description of filterLowCountGenes function. by jqsun <wukong@bi.a.u-tokyo.ac.jp> 2018-08-21 17:11:06 +0900;
34506c4 remove deseq2 option from DE test without replicates by jqsun <wukong@bi.a.u-tokyo.ac.jp> 2018-08-01 15:54:26 +0900;
2fae396 removed samseq options, since samr package has been removed from cran. by jqsun <wukong@bi.a.u-tokyo.ac.jp> 2018-07-31 16:14:03 +0900;
eaf13fa disabled SAMSeq options since samr package has been removed from CRAN. by jqsun <wukong@bi.a.u-tokyo.ac.jp> 2018-07-30 22:06:37 +0900;
021b4ec Fixed conflicts in version change by jqsun <wukong@bi.a.u-tokyo.ac.jp> 2018-06-11 14:49:47 +0900;
0ac4216 update version number. by jqsun <wukong@bi.a.u-tokyo.ac.jp> 2018-06-06 10:41:59 +0900;
04fc5f2 added annotations into baySeq countData object to sort the order of topCounts outputs. by jqsun <wukong@bi.a.u-tokyo.ac.jp> 2018-06-06 10:34:43 +0900;
182bbc8 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;
556c695 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 10:35:31 -0400;
3bdfe60 changed %d in sprintf to %.0f. by jqsun <wukong@bi.a.u-tokyo.ac.jp> 2017-11-28 12:12:12 +0900;
6d545f2 bump x.y.z versions to odd y after creation of RELEASE_3_6 branch by Hervé Pagès <hpages@fredhutch.org> 2017-10-30 12:52:53 -0400;
d13750f (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 12:40:07 -0400;
e5ce78a 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;
d26b8cb (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;
ae3149d 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;
b19ad19 deleted the imported function of baySeq::getPriors.BB in TCC NAMESPACE file. by Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp> 2017-01-11 23:02:06 +0000;
7da4c42 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;
db5bce7 (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;
cc1112a 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;
82ac6a7 update plot function. by Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp> 2016-05-26 02:27:50 +0000;
2557ced update plot function. by Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp> 2016-05-26 02:27:36 +0000;
30f9ac8 (origin/RELEASE_3_3, RELEASE_3_3) update plot function. by Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp> 2016-05-26 02:27:09 +0000;
3212c76 bump version after creating 3.3 branch by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-03 21:30:44 +0000;
d94bd96 Creating branch for BioC 3.3 release. by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-03 21:26:31 +0000;
9628062 Bump versions prior to creation of 3.3 branch by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-03 21:20:18 +0000;
b4dcfe5 fix warnings by Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp> 2016-05-03 06:08:49 +0000;
9b63076 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;
a27f086 (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;
e2dd14f Bumped versions of all packages prior to creating 3.2 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-10-13 19:36:05 +0000;
b67a197 add as.data.frame for edgeR results. (again) by Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp> 2015-09-29 09:29:01 +0000;
e56e2f4 (origin/RELEASE_3_1, RELEASE_3_1) add as.data.frame for edgeR results. (again) by Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp> 2015-09-29 09:28:54 +0000;
b5d81a5 add as.data.frame for the results from edgeR. by Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp> 2015-09-29 09:10:21 +0000;
2258210 add as.data.frame for the results from edgeR. by Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp> 2015-09-29 09:10:11 +0000;
bb0d8c3 update TCC. see NEWS for detailed. by Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp> 2015-09-08 01:51:52 +0000;
75a9845 changed the deafult 'xlab' and 'ylab' values in TCC.plotMA function. by Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp> 2015-07-16 08:58:53 +0000;
8b57c10 changed the deafult 'xlab' and 'ylab' values in TCC.plotMA function. by Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp> 2015-07-16 08:45:56 +0000;
a4340a7 changed R document by Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp> 2015-07-16 07:04:21 +0000;
ddf74fc changed R document by Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp> 2015-07-16 07:04:10 +0000;
287444a changed the default value of 'test.norm' when analyse multi group data without replicates. by Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp> 2015-07-16 05:48:24 +0000;
ffc8767 changed the default value of 'test.norm' when analyse multi group data without replicates. by Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp> 2015-07-16 05:47:59 +0000;
e9342af Bump versions in trunk after creation of 3.1 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-04-16 20:02:44 +0000;
3ec9faa Creating branch for BioC 3.1 release. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-04-16 20:00:01 +0000;
31c6c1b Bump versions prior to creating 3.1 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-04-16 19:42:01 +0000;
b97200c change the default method, from Wald to LRT, when test.methdo is specified to deseq2. by Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp> 2015-01-13 07:14:19 +0000;
428c2b3 fix bug in SAMseq by Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp> 2015-01-08 07:54:24 +0000;
558b773 bug fix in plotFCPseudocolor function. by Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp> 2015-01-04 03:03:34 +0000;
7b587ee (origin/RELEASE_3_0, RELEASE_3_0) bug fix in plotFCPseudocolor function by Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp> 2015-01-04 02:50:59 +0000;
4a146a3 bug fix in simulateReadCounts function. by Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp> 2015-01-04 02:01:05 +0000;
a1653f8 bug fix in simulateReadCounts functions. by Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp> 2015-01-04 01:57:56 +0000;
142b743 add MA coordinaets into results of DE analysis for paired two group by Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp> 2014-12-20 04:35:10 +0000;
e679064 change version by Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp> 2014-12-17 05:22:48 +0000;
eb39fc0 update plotMA by Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp> 2014-12-17 05:22:29 +0000;
3295298 minor update by Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp> 2014-12-11 11:52:06 +0000;
4f3c73d minor update by Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp> 2014-12-11 11:51:36 +0000;
ca60771 minor update by Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp> 2014-12-03 02:34:41 +0000;
b578c17 minor update, bug fix by Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp> 2014-12-01 06:43:31 +0000;
1ae5a36 upgrade a major improvement. by Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp> 2014-12-01 02:41:53 +0000;
e5d6fa4 fix bugs depends on baySeq changing. by Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp> 2014-10-20 23:59:00 +0000;