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ChangeLog
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ChangeLog
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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