Graph of compcodeR
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  • e1b50cd (HEAD -> devel, origin/devel, origin/HEAD) Update actions/cache by Charlotte Soneson <charlottesoneson@gmail.com> 2024-12-21 18:49:41 +0100;
  • fdc74f1 (origin/master) Merge remote-tracking branch 'upstream/devel' into devel by Charlotte Soneson <charlottesoneson@gmail.com> 2024-11-02 16:39:26 +0100;
  • a538f70 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 09:51:49 -0400;
  • 192bb4a (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 09:51:49 -0400;
  • 9ca6e9b Update upload-artifact action by Charlotte Soneson <charlottesoneson@gmail.com> 2024-07-14 22:29:32 +0200;
  • e5a2855 Use devel version of pak by Charlotte Soneson <charlottesoneson@gmail.com> 2024-05-18 09:49:41 +0200;
  • f304ec8 Use setup-r-dependencies action on Linux by Charlotte Soneson <charlottesoneson@gmail.com> 2024-05-17 09:31:29 +0200;
  • f54678b 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 10:36:17 -0400;
  • 5213459 (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 10:36:17 -0400;
  • d8f87e8 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 09:58:44 -0400;
  • 1bea8af (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 09:58:44 -0400;
  • f49091c Fix imports by Charlotte Soneson <charlottesoneson@gmail.com> 2023-09-28 13:02:09 +0200;
  • 58f4d83 Merge pull request <a href="#20">#20</a> from csoneson/shinygui by Charlotte Soneson <charlottesoneson@gmail.com> 2023-09-24 11:06:10 +0200;
  • 6ca173b Update NEWS by Charlotte Soneson <charlottesoneson@gmail.com> 2023-09-24 11:05:43 +0200;
  • fa599f8 Fix message by Charlotte Soneson <charlottesoneson@gmail.com> 2023-09-22 17:23:04 +0200;
  • 16b3dc6 Fix typos by Charlotte Soneson <charlottesoneson@gmail.com> 2023-07-03 20:10:13 +0200;
  • 60ac6a1 Document runComparisonShiny by Charlotte Soneson <charlottesoneson@gmail.com> 2023-07-03 19:41:27 +0200;
  • c76bdcd Remove baySeq (deprecated) by Charlotte Soneson <charlottesoneson@gmail.com> 2023-07-03 19:37:48 +0200;
  • 9484c0c Swap markdown::markdownToHTML for rmarkdown::pandoc_convert by Charlotte Soneson <charlottesoneson@gmail.com> 2023-07-03 19:16:03 +0200;
  • b4dfc5a Fix imports by Charlotte Soneson <charlottesoneson@gmail.com> 2023-07-03 16:54:45 +0200;
  • 9c29bec Merge branch 'devel' into shinygui by Charlotte Soneson <charlottesoneson@gmail.com> 2023-07-03 16:24:07 +0200;
  • 5d5855a (origin/RELEASE_3_17, RELEASE_3_17) Fix phylolm.factor test error by Charlotte Soneson <charlottesoneson@gmail.com> 2023-07-03 16:23:42 +0200;
  • e7b809e Version bump by Charlotte Soneson <charlottesoneson@gmail.com> 2023-07-03 16:21:36 +0200;
  • ce991b7 Move tcltk and sm to Suggests by Charlotte Soneson <charlottesoneson@gmail.com> 2023-07-03 16:17:57 +0200;
  • 723a017 Merge pull request <a href="#19">#19</a> from pbastide/phylolm_factor_win by Charlotte Soneson <charlottesoneson@gmail.com> 2023-07-03 16:14:35 +0200;
  • 98b252d Trying phylolm.factor with measurement error by Paul Bastide <paul.bastide@m4x.org> 2023-07-03 09:46:41 +0200;
  • 5c5a56c Merge remote-tracking branch 'upstream/devel' into devel by Paul Bastide <paul.bastide@m4x.org> 2023-07-03 07:36:32 +0200;
  • d37689d Merge branch 'devel' into shinygui by Charlotte Soneson <charlottesoneson@gmail.com> 2023-06-30 12:39:41 +0200;
  • 56259d3 Exclude test giving invalid Windows file name by Charlotte Soneson <charlottesoneson@gmail.com> 2023-06-28 13:22:36 +0200;
  • 54b4671 Bump version by Charlotte Soneson <charlottesoneson@gmail.com> 2023-06-28 13:20:36 +0200;
  • 8e7b7f7 Clean up by Charlotte Soneson <charlottesoneson@gmail.com> 2023-06-25 09:55:00 +0200;
  • 5c2b812 Remove phylolm.factor from generateCodeHTML test by Charlotte Soneson <charlottesoneson@gmail.com> 2023-06-25 09:11:16 +0200;
  • 52ad9c3 GHA: Reorder methods by Charlotte Soneson <charlottesoneson@gmail.com> 2023-06-25 08:46:31 +0200;
  • 19c867e GHA: print method/file names for code generation by Charlotte Soneson <charlottesoneson@gmail.com> 2023-06-24 20:49:00 +0200;
  • 0ed57a1 GHA: Update gfortran symlink by Charlotte Soneson <charlottesoneson@gmail.com> 2023-06-24 20:30:50 +0200;
  • bab6413 Merge remote-tracking branch 'upstream/devel' into devel by Paul Bastide <paul.bastide@m4x.org> 2023-05-23 13:23:01 +0200;
  • 7f75f7c Update GHA workflow by Charlotte Soneson <charlottesoneson@gmail.com> 2023-05-13 09:30:56 +0200;
  • e1b28df 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 10:31:47 -0400;
  • d667873 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 10:31:47 -0400;
  • 98f38b6 Merge pull request <a href="#16">#16</a> from pbastide/sva by Charlotte Soneson <charlottesoneson@gmail.com> 2022-11-09 15:44:38 +0100;
  • 24bc4b6 Clean-up and bump version by Paul Bastide <paul.bastide@gmail.com> 2022-11-09 14:41:00 +0100;
  • 44c71fb Merge branch 'master' into sva by Paul Bastide <paul.bastide@gmail.com> 2022-11-07 09:31:27 +0100;
  • 9130305 Test for correct variable in sva analysis. by Paul Bastide <paul.bastide@gmail.com> 2022-11-02 19:09:28 +0100;
  • ec6272c Merge remote-tracking branch 'upstream/master' by Charlotte Soneson <charlottesoneson@gmail.com> 2022-11-01 21:53:24 +0100;
  • b978c66 Add SVA analysis by Paul Bastide <paul.bastide@gmail.com> 2022-11-01 17:33:50 +0100;
  • dfd6faa 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 11:09:36 -0400;
  • 0febb89 (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 11:09:36 -0400;
  • 3a976d3 Change version of r-lib action by Charlotte Soneson <charlottesoneson@gmail.com> 2022-10-21 11:08:48 +0200;
  • aba6206 (origin/RELEASE_3_15, RELEASE_3_15) Version bump by Charlotte Soneson <charlottesoneson@gmail.com> 2022-09-22 17:19:19 +0200;
  • eba9878 Increase tolerence for highly variable counts. by Paul Bastide <paul.bastide@gmail.com> 2022-09-19 19:51:45 +0200;
  • 98ff874 Use inherits for S3 class. by Paul Bastide <paul.bastide@gmail.com> 2022-09-19 19:31:24 +0200;
  • 9717107 Version bump by Charlotte Soneson <charlottesoneson@gmail.com> 2022-09-20 15:57:34 +0200;
  • 4c2a8b3 Merge pull request <a href="#15">#15</a> from pbastide/master by Charlotte Soneson <charlottesoneson@gmail.com> 2022-09-20 15:53:59 +0200;
  • 0968bcf Increase tolerence for highly variable counts. by Paul Bastide <paul.bastide@gmail.com> 2022-09-19 19:51:45 +0200;
  • 710a557 Use inherits for S3 class. by Paul Bastide <paul.bastide@gmail.com> 2022-09-19 19:31:24 +0200;
  • 495ccb2 Merge remote-tracking branch 'upstream/master' by Paul Bastide <paul.bastide@gmail.com> 2022-09-19 18:53:29 +0200;
  • 67abd7f Use bioc actions by Charlotte Soneson <charlottesoneson@gmail.com> 2022-04-30 11:27:02 +0200;
  • 2f26264 Merge remote-tracking branch 'upstream/master' by Charlotte Soneson <charlottesoneson@gmail.com> 2022-04-30 11:22:17 +0200;
  • 748016a 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 15:19:31 +0000;
  • 9d33fad 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 15:19:31 +0000;
  • 018cc8e Set bitmapType by Charlotte Soneson <charlottesoneson@gmail.com> 2022-02-20 10:56:25 +0100;
  • 230de4e Merge remote-tracking branch 'upstream/master' by Paul Bastide <paul.bastide@gmail.com> 2022-01-24 16:02:58 +0100;
  • 730c4d0 Merge pull request <a href="#14">#14</a> from csoneson/phylocomp by Charlotte Soneson <charlottesoneson@gmail.com> 2022-01-24 12:27:05 +0100;
  • 361f261 Bump version by Charlotte Soneson <charlottesoneson@gmail.com> 2022-01-24 11:21:35 +0100;
  • 33b9959 Add runComparisonShiny by Charlotte Soneson <charlottesoneson@gmail.com> 2022-01-24 11:20:10 +0100;
  • 406040b Merge pull request <a href="#13">#13</a> from pbastide/toCompcodeR by Charlotte Soneson <charlottesoneson@gmail.com> 2022-01-24 11:16:32 +0100;
  • faffdef Update citation with preprint. by Paul Bastide <paul.bastide@gmail.com> 2022-01-24 09:15:02 +0100;
  • e646f44 Merge pull request <a href="#11">#11</a> from pbastide/toCompcodeR by Charlotte Soneson <charlottesoneson@gmail.com> 2021-11-30 20:05:50 +0100;
  • 0c1f4e7 DESeq2.length.results -> DESeq2.results by Paul Bastide <paul.bastide@gmail.com> 2021-11-30 10:58:17 +0100;
  • 82ffb87 More param inheritance. by Paul Bastide <paul.bastide@gmail.com> 2021-11-25 09:20:06 +0100;
  • 34d9948 Add nas.as.ones in DESeq2.createRmd and remove some roxygen redundancy. by Paul Bastide <paul.bastide@gmail.com> 2021-11-25 09:11:10 +0100;
  • d7b7444 nas_as_ones -> nas.as.ones by Paul Bastide <paul.bastide@gmail.com> 2021-11-24 17:03:23 +0100;
  • 3fba209 Dependency on phytools for tests. by Paul Bastide <paul.bastide@gmail.com> 2021-11-24 11:08:09 +0100;
  • fd26b74 Allow prop.var.tree to be a vector. by Paul Bastide <paul.bastide@gmail.com> 2021-11-24 10:21:37 +0100;
  • ebe2728 Add message for nas_to_ones argument. by Paul Bastide <paul.bastide@gmail.com> 2021-11-22 18:28:23 +0100;
  • 30f98c4 Add an option to set NAs padj to 1 in DESeq2. by Paul Bastide <paul.bastide@gmail.com> 2021-11-22 10:11:33 +0100;
  • 49e6ea8 Add some correlation tests by Paul Bastide <paul.bastide@gmail.com> 2021-11-22 09:33:09 +0100;
  • b877840 rpois_robust is not needed since R 4.0 by Paul Bastide <paul.bastide@gmail.com> 2021-11-22 09:12:53 +0100;
  • 3d2c379 Correct error in rpois_robust by Paul Bastide <paul.bastide@gmail.com> 2021-11-22 09:08:54 +0100;
  • 2554cd8 Remove dependency to viridis package. by Paul Bastide <paul.bastide@gmail.com> 2021-11-22 09:07:31 +0100;
  • 44a82c9 Safeguarding in the data summary report by Charlotte Soneson <charlottesoneson@gmail.com> 2021-11-10 18:05:12 +0100;
  • 1648beb Merge pull request <a href="#10">#10</a> from pbastide/toCompcodeR by Charlotte Soneson <charlottesoneson@gmail.com> 2021-11-06 09:16:22 +0100;
  • e5dabd2 Add statmod in suggest, required for correlation modelling in limma. by Paul Bastide <paul.bastide@gmail.com> 2021-11-03 11:45:31 +0100;
  • feb8c2c More tests and correction in covariate handling. by Paul Bastide <paul.bastide@gmail.com> 2021-11-03 09:27:42 +0100;
  • 5d0fb6d More tests. by Paul Bastide <paul.bastide@gmail.com> 2021-11-02 16:07:08 +0100;
  • aef6c7a Test and slight refactor on phyloCompData class checks. by Paul Bastide <paul.bastide@gmail.com> 2021-11-02 16:06:53 +0100;
  • 69d793d Add covr in suggest by Paul Bastide <paul.bastide@gmail.com> 2021-11-02 11:49:58 +0100;
  • a2e847e Add tests for generateSyntheticData and runDiffExpr with phylo tree. by Paul Bastide <paul.bastide@gmail.com> 2021-11-02 11:00:50 +0100;
  • 67375b3 Remove deprecated option from phylolm. by Paul Bastide <paul.bastide@gmail.com> 2021-11-02 10:01:24 +0100;
  • 90a4ef7 Merge remote-tracking branch 'upstream/master' by Paul Bastide <paul.bastide@gmail.com> 2021-11-02 09:49:31 +0100;
  • 2ef38b1 Updates from upstream by Charlotte Soneson <charlottesoneson@gmail.com> 2021-10-30 14:25:32 +0200;
  • 7d50e69 Use ubuntu-latest on GHA by Charlotte Soneson <charlottesoneson@gmail.com> 2021-10-30 14:22:29 +0200;
  • d22c179 Use R devel on GHA by Charlotte Soneson <charlottesoneson@gmail.com> 2021-10-30 14:20:16 +0200;
  • 2b73324 Merge remote-tracking branch 'upstream/master' by Charlotte Soneson <charlottesoneson@gmail.com> 2021-10-27 08:42:17 +0200;
  • 8a1ba36 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 16:13:18 +0000;
  • bd52d89 (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 16:13:18 +0000;
  • d9683d2 Use ubuntu-latest on GHA by Charlotte Soneson <charlottesoneson@gmail.com> 2021-10-24 21:51:41 +0200;
  • 541ad97 Merge pull request <a href="#8">#8</a> from pbastide/toCompcodeR by Charlotte Soneson <charlottesoneson@gmail.com> 2021-10-24 21:48:58 +0200;
  • a0911fd Change version to 1.29.1 by Paul Bastide <paul.bastide@gmail.com> 2021-10-22 16:06:05 +0200;
  • b75ae90 Skip tests individually by Paul Bastide <paul.bastide@gmail.com> 2021-10-04 12:36:26 +0200;