Version 0.50.08, 28.7.2022 * Corrected a small bug in evidencePlot Version 0.50.06, 9.6.2022 * Corrected a severe bug Version 0.50 * Optimized memory usage Version 0.44, 22.5.2020 * added leading edge analysis * added upset plots Version 0.43, 17.4.2020 * in tmodPanelPlot and pvalEffectPlot, modified the defaults such that it is now possible to use blue and red dots if the effect sizes are both smaller and larger than 0 (e.g. NES instead of AUC) * modified tmodSummary such that effect size and p value columns can be specifieed * result of tmodSummary is now an S3 class * modified tmodPanelPlot such that it can directly take the result of tmodSummary Version 0.42, 5.3.2020 * Updated tmodPCA & co * Added colors to evidence plots Version 0.40, 28.11.2018 * Added tmodGeneSetTest * Updated users manual Version 0.39, 18.09.2018 * Added tmodPLAGEtest Version 0.38, 28.03.2018: * corrected several bugs (including problems with painting labels) * moved most of the vignette to the user guide, which can be displayed with tmodUserGuide() Version 0.37, 9.03.2018: * added functions eigengene, modcors and modjaccard Version 0.36, 09.03.2018: * corrected notorious problems with CRAN * please CRAN have mercy * I will sacrifice a virtual goat before submitting * changed parameter "order.by" to "sort.by" in tmodLimmaTest * added function pcaplot; tmod no longer depends on pca3d due to notorious problems with installing rgl on students Mac computers * limma examples now wrapped in if(require(limma))... Version 0.35 * corrected a bug in behavior of filter.rows.auc Version 0.34, 10.08.2017: * added filter.rows.auc option Version 0.32: * Added tmodZtest and tmodWZtest * Modified gene.labels option for evidencePlot Version 0.31: * Use of the plotwidgets package for pvalEffectPlot (rug, boxpie and pie options) Version 0.30: * Apparently, knitr cache got packed in the package itself, blowing up its size ten fold. Version 0.29: * A last minute bugfix Version 0.28: * Added simpleBoxpie - rectangular plots that are thought better to visualize areas than regular pie charts * added a few palette functions from my personal repertoire Version 0.27: * Introduced metabolic modules and created a vignette section for a case study in metabolomic * changed the return object of tmodPCA() * added the "extra" parameter to showModule(); showModule() can take a data frame or a vector now * added "row.labels.style" parameter to tmodPanelPlot() Version 0.25: * corrected the malfunctioning testthat test. I HATE TESTTHAT. (Also, I read it as "test t hat" - and wonder about estimates and Student's t) Version 0.24: * msigDB is broken, it no longer has unique identifiers in the global XML file. I corrected the import function to make sure identifiers are unique. * pvalEffectPlot was expecting log10(p-values) rather than p-values. This has been taken care of. * evidencePlot can now generate GSEA-style curves (with the "style" option) Version 0.22: * added Cohen's d estimate and t statistic to tmodLimmaTopTable() * rewrote evidencePlot: it is now much more flexible