1. GeneTonic
  2. Graph
Graph of GeneTonic
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  • 4336f49 (HEAD -> devel, origin/master, origin/devel, origin/HEAD, master) 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;
  • bf4969a version bump, 2.1.1 by Federico Marini <marinif@uni-mainz.de> 2022-05-01 10:59:16 +0200;
  • c192ce4 updating citation(s) for the package by Federico Marini <marinif@uni-mainz.de> 2022-05-01 10:57:49 +0200;
  • 29295b2 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 16:02:24 +0000;
  • f15fe5f 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 16:02:24 +0000;
  • ca561a1 Merge pull request <a href="#28">#28</a> from federicomarini/gtl_at_runtime by Federico Marini <marinif@uni-mainz.de> 2022-04-06 13:18:23 +0200;
  • 69b94e9 version bump, 1.99.3 by Federico Marini <marinif@uni-mainz.de> 2022-04-06 13:04:19 +0200;
  • bac708b fixing typo and re-rendering manpages by Federico Marini <marinif@uni-mainz.de> 2022-04-06 12:07:44 +0200;
  • 0204ac2 updated news by Federico Marini <marinif@uni-mainz.de> 2022-04-06 12:07:19 +0200;
  • be6f118 Version bump, 1.99.2 by Federico Marini <marinif@uni-mainz.de> 2022-04-04 17:26:14 +0200;
  • aeb61f0 expanding tour about GeneSpector component by Federico Marini <marinif@uni-mainz.de> 2022-04-04 17:22:17 +0200;
  • adc0b0a additional content about the upload functionality in the vignette by Federico Marini <marinif@uni-mainz.de> 2022-04-04 17:11:05 +0200;
  • 7e7ee14 adding specific example for GeneTonic run without input data by Federico Marini <marinif@uni-mainz.de> 2022-04-04 17:10:48 +0200;
  • df4db08 fixing the help for gtl upload by Federico Marini <marinif@uni-mainz.de> 2022-04-04 17:10:31 +0200;
  • 61fff72 rerendered manpage by Federico Marini <marinif@uni-mainz.de> 2022-03-30 15:00:58 +0200;
  • 3f88564 one round of styler on recent R source files by Federico Marini <marinif@uni-mainz.de> 2022-03-30 15:00:28 +0200;
  • ada1cfb Version bump, 1.99.1 by Federico Marini <marinif@uni-mainz.de> 2022-03-30 12:16:01 +0200;
  • 96def07 updated NEWS.md by Federico Marini <marinif@uni-mainz.de> 2022-03-30 12:15:50 +0200;
  • 76862dc Merge pull request <a href="#33">#33</a> from federicomarini/gsupset by Federico Marini <marinif@uni-mainz.de> 2022-03-30 12:11:52 +0200;
  • 20e8261 fixing example by Federico Marini <marinif@uni-mainz.de> 2022-03-30 12:11:00 +0200;
  • ee5589f Merge pull request <a href="#32">#32</a> from federicomarini/gsupset by Federico Marini <marinif@uni-mainz.de> 2022-03-30 12:05:07 +0200;
  • 77da2f0 full suite of unit tests for the gs_upset functionality by Federico Marini <marinif@uni-mainz.de> 2022-03-30 11:58:59 +0200;
  • b14ee13 updated testing setup by Federico Marini <marinif@uni-mainz.de> 2022-03-30 11:58:40 +0200;
  • 1971f76 added manpages for upset related functionality by Federico Marini <marinif@uni-mainz.de> 2022-03-30 11:58:28 +0200;
  • 9d5079e added functionality to plot geneset upset plots by Federico Marini <marinif@uni-mainz.de> 2022-03-30 11:58:00 +0200;
  • e734002 updated news by Federico Marini <marinif@uni-mainz.de> 2022-03-29 12:55:58 +0200;
  • 3a5df49 Version bump, 1.99.0 by Federico Marini <marinif@uni-mainz.de> 2022-03-28 17:42:56 +0200;
  • 826e602 Updated news by Federico Marini <marinif@uni-mainz.de> 2022-03-28 17:42:41 +0200;
  • d71f130 Merge branch 'gtl_at_runtime' of github.com:federicomarini/GeneTonic into gtl_at_runtime by Federico Marini <marinif@uni-mainz.de> 2022-03-28 16:52:36 +0200;
  • b607442 Completing text section for the help in the data upload section by Federico Marini <marinif@uni-mainz.de> 2022-03-28 16:52:18 +0200;
  • 1afd76c adding vignette screenshot by Federico Marini <marinif@uni-mainz.de> 2022-03-28 16:51:55 +0200;