1. GeneTonic
  2. Graph
Graph of GeneTonic
  • *
  • *
  • | *
  • | |\
  • | |/
  • |/|
  • * |
  • |\ \
  • * | |
  • * | |
  • | * |
  • |/| |
  • | * |
  • |/ /
  • | *
  • | |\
  • | |/
  • |/|
  • | *
  • | *
  • | *
  • * |
  • * |
  • * |
  • * |
  • * |
  • * |
  • * |
  • * |
  • |/
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • |\
  • | *
  • | *
  • * |
  • |\ \
  • | | *
  • | | *
  • | | *
  • | | *
  • | |/
  • | *
  • | *
  • | *
  • | *
  • | *
  • | *
  • | *
  • | *
  • |/
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • |\
  • | *
  • * |
  • |\ \
  • | | *
  • | | *
  • | | *
  • | | *
  • | | *
  • | | *
  • | | *
  • | | *
  • | | *
  • | | *
  • | | *
  • | | *
  • | |/
  • | *
  • | |\
  • | |/
  • |/|
  • * |
  • * |
  • * |
  • * |
  • | *
  • | *
  • | *
  • | *
  • | *
  • | *
  • | *
  • |/
  • *
  • | *
  • | *
  • | *
  • * |
  • |\ \
  • | * |
  • | * |
  • | * |
  • |/ /
  • * |
  • | *
  • | *
  • | *
  • | *
  • * |
  • |\ \
  • | * |
  • * | |
  • |\| |
  • | * |
  • | * |
  • | * |
  • | * |
  • |/ /
  • 365e9d8 (HEAD -> devel, origin/master, origin/devel, origin/HEAD) 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 11:19:17 -0400;
  • c3f7778 (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 11:19:17 -0400;
  • 55e4ea5 (origin/RELEASE_3_17, RELEASE_3_17) Merge branch 'devel' into RELEASE_3_17 by Federico Marini <marinif@uni-mainz.de> 2023-09-28 16:09:47 +0200;
  • 51bc3bb Merge branch 'devel' of github.com:federicomarini/GeneTonic into devel by Federico Marini <marinif@uni-mainz.de> 2023-09-28 16:07:56 +0200;
  • 0c54cb6 version bump, 2.5.2 by Federico Marini <marinif@uni-mainz.de> 2023-09-28 16:07:47 +0200;
  • 2e85bd1 updated news by Federico Marini <marinif@uni-mainz.de> 2023-09-28 16:07:37 +0200;
  • c816d29 Merge pull request <a href="#55">#55</a> from federicomarini/fix_gs_scores by Federico Marini <marinif@uni-mainz.de> 2023-09-28 16:06:01 +0200;
  • 12cd01d force keeping the data frame structure to enable colMeans to keep on working by Federico Marini <marinif@uni-mainz.de> 2023-09-28 11:59:52 +0200;
  • 2fd91eb Merge remote-tracking branch 'upstream/devel' into RELEASE_3_17 by Federico Marini <marinif@uni-mainz.de> 2023-08-10 12:54:14 +0200;
  • 9f5063d version bump, 2.4.1 for bugfix by Federico Marini <marinif@uni-mainz.de> 2023-08-10 12:51:05 +0200;
  • 017c048 updated news by Federico Marini <marinif@uni-mainz.de> 2023-08-10 12:48:29 +0200;
  • 5f8e1fe whoopsie, swapped the signs. Inverting the < and > signs for the summary description of the gtl object by Federico Marini <marinif@uni-mainz.de> 2023-08-10 12:46:59 +0200;
  • a874402 version bump, 2.5.1 by Federico Marini <marinif@uni-mainz.de> 2023-08-10 12:49:08 +0200;
  • f2e6106 updated news by Federico Marini <marinif@uni-mainz.de> 2023-08-10 12:48:29 +0200;
  • 4a3bb1c whoopsie, swapped the signs. Inverting the < and > signs for the summary description of the gtl object by Federico Marini <marinif@uni-mainz.de> 2023-08-10 12:46:59 +0200;
  • af9d097 removing gfortran from GHA o_O by Federico Marini <marinif@uni-mainz.de> 2023-05-05 11:46:22 +0200;
  • b4d56ce updating gfortran in github action by Federico Marini <marinif@uni-mainz.de> 2023-05-05 11:36:24 +0200;
  • b1a834b fixed readme with logo and badges by Federico Marini <marinif@uni-mainz.de> 2023-04-28 23:01:52 +0200;
  • 70fcec3 added logo for pkgdown by Federico Marini <marinif@uni-mainz.de> 2023-04-28 23:01:36 +0200;
  • 5e6b0a1 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 11:15:16 -0400;
  • 41dd44e 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 11:15:16 -0400;
  • 6bff9f9 version bump, 2.3.4 by Federico Marini <marinif@uni-mainz.de> 2023-04-22 14:15:38 +0200;
  • 452034d updated news by Federico Marini <marinif@uni-mainz.de> 2023-04-22 14:15:12 +0200;
  • 8e9aa5c behavior mirrored also for the genespector box by Federico Marini <marinif@uni-mainz.de> 2023-04-22 14:15:06 +0200;
  • f85b196 adding option to display or hide labels in the output generated by gene_plot by Federico Marini <marinif@uni-mainz.de> 2023-04-22 14:13:24 +0200;
  • 08da071 adjusting imports for tippy by Federico Marini <marinif@uni-mainz.de> 2023-04-22 13:17:59 +0200;
  • 0acdd0a code popups to be visualized correctly again - tippy changed in between by Federico Marini <marinif@uni-mainz.de> 2023-04-22 13:17:46 +0200;
  • cc7da88 writing a bit more in the DESCRIPTION by Federico Marini <marinif@uni-mainz.de> 2023-04-22 13:17:20 +0200;
  • c0202ac version bump, 2.3.3 by Federico Marini <marinif@uni-mainz.de> 2023-04-20 21:07:23 +0200;
  • ed7eb92 Added ShinyApps to biocViews by Federico Marini <marinif@uni-mainz.de> 2023-04-20 21:07:03 +0200;
  • 4336f49 Merge pull request <a href="#48">#48</a> from federicomarini/fortified_geneplot by Federico Marini <marinif@uni-mainz.de> 2023-03-14 15:34:59 +0100;
  • a8448d1 version bump, 2.3.2 by Federico Marini <marinif@uni-mainz.de> 2023-03-10 16:07:13 +0100;
  • af6310f updated news by Federico Marini <marinif@uni-mainz.de> 2023-03-10 16:06:48 +0100;
  • 0484084 Merge pull request <a href="#47">#47</a> from federicomarini/ridge_genesets by Federico Marini <marinif@uni-mainz.de> 2023-03-10 16:06:32 +0100;
  • 5a55130 extending test suite for the latest changes, triggering error for gene_plot by Federico Marini <marinif@uni-mainz.de> 2023-03-10 16:05:50 +0100;
  • 9187eb9 adding extra check on the intgroup parameter to make sure it is encoded in the data to be plotted by Federico Marini <marinif@uni-mainz.de> 2023-03-10 16:05:30 +0100;
  • 3768604 updated news by Federico Marini <marinif@uni-mainz.de> 2023-03-10 15:27:17 +0100;
  • 36f85d0 version bump, 2.3.1 by Federico Marini <marinif@uni-mainz.de> 2023-03-10 15:16:25 +0100;
  • 3347231 extending code coverage to 100% again, some edge cases in gs_dendro by Federico Marini <marinif@uni-mainz.de> 2023-01-30 16:21:25 +0100;
  • 144447c re-rendering manpages by Federico Marini <marinif@uni-mainz.de> 2023-01-30 15:10:10 +0100;
  • b434629 fixing tidyselect warnings in the unit tests by Federico Marini <marinif@uni-mainz.de> 2023-01-30 15:10:03 +0100;
  • 8766323 extending test suite for enhance_table by Federico Marini <marinif@uni-mainz.de> 2023-01-30 15:07:35 +0100;
  • 65fd9ea changing param name as size is deprecated for geom_line by Federico Marini <marinif@uni-mainz.de> 2023-01-30 15:07:05 +0100;
  • 55c3e67 updating imports from ggridges to pass flawlessly R CMD check by Federico Marini <marinif@uni-mainz.de> 2023-01-30 15:06:42 +0100;
  • f970dc3 expanding the functionality of enhance_table, with the geneset ridge lines (option for coloring them) by Federico Marini <marinif@uni-mainz.de> 2023-01-30 14:54:35 +0100;
  • 1b0f4b6 updating roxygen version by Federico Marini <marinif@uni-mainz.de> 2023-01-30 14:53:32 +0100;
  • c32b540 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 11:21:18 -0400;
  • cbc0a9f (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 11:21:18 -0400;
  • ef97f2a version bump, 2.1.7 by Federico Marini <marinif@uni-mainz.de> 2022-10-29 15:25:24 +0200;
  • d262193 avoiding using FA icons as buttons in the vignette, after recent changes in the fontawesome package breaking the build by Federico Marini <marinif@uni-mainz.de> 2022-10-29 15:24:44 +0200;
  • 2ee139c updating GHA version linked by Federico Marini <marinif@uni-mainz.de> 2022-10-20 11:44:52 +0200;
  • 9a5bc27 version bump, 2.1.6 by Federico Marini <marinif@uni-mainz.de> 2022-10-20 11:43:05 +0200;
  • d1a1d48 fixing namespace after backbone updates by Federico Marini <marinif@uni-mainz.de> 2022-10-20 11:39:44 +0200;
  • 6e4a5e2 Merge pull request <a href="#43">#43</a> from federicomarini/better_colors by Federico Marini <marinif@uni-mainz.de> 2022-10-07 16:54:01 +0200;
  • ba00c6f removing extra --- in the vignette, putting a <hr> tag by Federico Marini <marinif@uni-mainz.de> 2022-10-07 16:01:42 +0200;
  • f9096e0 Merge pull request <a href="#42">#42</a> from federicomarini/heatmap_winsorized by Federico Marini <marinif@uni-mainz.de> 2022-10-07 15:26:45 +0200;
  • 63998e9 version bump, 2.1.5 by Federico Marini <marinif@uni-mainz.de> 2022-10-07 15:26:19 +0200;
  • cf6a2c2 updating news by Federico Marini <marinif@uni-mainz.de> 2022-10-07 15:26:11 +0200;
  • dd9ad84 fixing test for positive-zscores only subset by Federico Marini <marinif@uni-mainz.de> 2022-10-07 14:42:32 +0200;
  • c161825 cleanups and na.omit()ting by Federico Marini <marinif@uni-mainz.de> 2022-10-07 14:25:37 +0200;
  • 8026293 fixing graph backbone function where NAs are around by Federico Marini <marinif@uni-mainz.de> 2022-10-07 14:25:19 +0200;
  • 4ca0178 giving neutral color to NA values in the emap as well by Federico Marini <marinif@uni-mainz.de> 2022-10-07 13:52:07 +0200;
  • 40ea094 specifying to omit the NA from the ranges calculations by Federico Marini <marinif@uni-mainz.de> 2022-10-07 13:42:32 +0200;
  • c21088d manpage re-rendered by Federico Marini <marinif@uni-mainz.de> 2022-10-07 13:31:56 +0200;
  • e5e3257 gs dendrogram also better respecting the range of values for mapping to values by Federico Marini <marinif@uni-mainz.de> 2022-10-07 13:31:48 +0200;
  • db4ae46 changing example way of presenting the enrichment map in the vignette by Federico Marini <marinif@uni-mainz.de> 2022-10-07 13:20:26 +0200;
  • fe3cb4d enrichment map colors are handled respecting better the range of values by Federico Marini <marinif@uni-mainz.de> 2022-10-07 13:20:09 +0200;
  • 9d66329 map2color gains the option of becoming symmetrical to the extreme values - useful if these are diverging by Federico Marini <marinif@uni-mainz.de> 2022-10-07 13:18:59 +0200;
  • 6b931c4 Merge branch 'master' into heatmap_winsorized by Federico Marini <marinif@uni-mainz.de> 2022-10-06 18:13:21 +0200;
  • f22ba73 version bump, 2.1.4 by Federico Marini <marinif@uni-mainz.de> 2022-10-05 21:01:20 +0200;
  • 1578954 updated NEWS by Federico Marini <marinif@uni-mainz.de> 2022-10-05 21:01:06 +0200;
  • e6abb60 extending the test suite to cover the case where a gene is in the enrichment results table but not present in the annotation (e.g. annotations are updated, so some correspondences might get lost) by Federico Marini <marinif@uni-mainz.de> 2022-10-05 20:58:55 +0200;
  • 8f90912 * preventing genes not included in the annotation to trigger an error if NA - no match were found. * also presents an informative message on which genesets/genes are potentially responsible by Federico Marini <marinif@uni-mainz.de> 2022-10-05 20:57:57 +0200;
  • aac6649 fixed indenting by Federico Marini <marinif@uni-mainz.de> 2022-10-04 10:54:05 +0200;
  • b9ece33 version bump, 2.1.4 by Federico Marini <marinif@uni-mainz.de> 2022-09-21 17:29:53 +0200;
  • af1ca8f updated news by Federico Marini <marinif@uni-mainz.de> 2022-09-21 17:29:43 +0200;
  • 7edf46a test suite extended to cover also some examples of winsorizing the vst expression data by Federico Marini <marinif@uni-mainz.de> 2022-09-21 17:14:05 +0200;
  • 4ea2216 extending documentation with some suggested values by Federico Marini <marinif@uni-mainz.de> 2022-09-21 17:07:57 +0200;
  • 0ab557e re-rendering manpage by Federico Marini <marinif@uni-mainz.de> 2022-09-21 17:04:52 +0200;
  • ee025e9 adding parameter and functionality to do some basic winsorization on the heatmap values by Federico Marini <marinif@uni-mainz.de> 2022-09-21 17:04:39 +0200;
  • ce8572a bump roxygen version by Federico Marini <marinif@uni-mainz.de> 2022-09-07 17:50:19 +0200;
  • 19e79ae (origin/RELEASE_3_15, RELEASE_3_15) version bump, 2.0.2 for release bugfix by Federico Marini <marinif@uni-mainz.de> 2022-08-03 10:42:03 +0200;
  • bdd08d7 updated news by Federico Marini <marinif@uni-mainz.de> 2022-08-03 10:37:44 +0200;
  • f7e8a67 fixed the row names on the heatmap, now taking the gene_id column from the anno_df instead of the rownames by Annekathrin Silvia Ludt <annekathrin@zdv-vpn01-38-62.zdv.Uni-Mainz.DE> 2022-08-02 15:32:21 +0200;
  • 2bdf9b4 Merge pull request <a href="#38">#38</a> from federicomarini/heatmap_fix by Federico Marini <marinif@uni-mainz.de> 2022-08-03 10:38:09 +0200;
  • 4fa283a version bump, 2.1.3 by Federico Marini <marinif@uni-mainz.de> 2022-08-03 10:37:53 +0200;
  • d694bc2 updated news by Federico Marini <marinif@uni-mainz.de> 2022-08-03 10:37:44 +0200;
  • 70c8619 fixed the row names on the heatmap, now taking the gene_id column from the anno_df instead of the rownames by Annekathrin Silvia Ludt <annekathrin@zdv-vpn01-38-62.zdv.Uni-Mainz.DE> 2022-08-02 15:32:21 +0200;
  • 11c851b updated NEWS by Federico Marini <marinif@uni-mainz.de> 2022-06-10 16:22:06 +0200;
  • 6d01cdf updated NEWS by Federico Marini <marinif@uni-mainz.de> 2022-06-10 16:22:06 +0200;
  • e3c9ea0 Version bump, 2.0.1 by Federico Marini <marinif@uni-mainz.de> 2022-06-10 16:20:53 +0200;
  • f4fda95 updating citation(s) for the package by Federico Marini <marinif@uni-mainz.de> 2022-05-01 10:57:49 +0200;
  • f6814b3 fixing the usage of reactive element after aggregating the scores on the fly by Federico Marini <marinif@uni-mainz.de> 2022-05-19 19:50:05 +0200;
  • 2e2b98a Merge pull request <a href="#36">#36</a> from federicomarini/reacto_fix by Federico Marini <marinif@uni-mainz.de> 2022-05-27 16:08:38 +0200;
  • a6b0f49 update gh actions by Federico Marini <marinif@uni-mainz.de> 2022-05-27 16:08:07 +0200;
  • d14e3c1 Merge pull request <a href="#35">#35</a> from federicomarini/reacto_fix by Federico Marini <marinif@uni-mainz.de> 2022-05-27 16:07:35 +0200;
  • b42640a updating gh actions to use Mike's with specific Bioc versioning by Federico Marini <marinif@uni-mainz.de> 2022-05-27 15:16:01 +0200;
  • 7fbd484 version bump, 2.1.2 by Federico Marini <marinif@uni-mainz.de> 2022-05-19 20:15:24 +0200;
  • f5953af updating roxygen version number, while we are at it by Federico Marini <marinif@uni-mainz.de> 2022-05-19 19:53:36 +0200;
  • f1cc8fe fixing the usage of reactive element after aggregating the scores on the fly by Federico Marini <marinif@uni-mainz.de> 2022-05-19 19:50:05 +0200;