NEWS

POMA 1.17.6

New POMA theme and colorblind-friendly palette
Available sample normalization (sum and quantile)
New feature normalization methods
Extensive review and improvement of all POMA functions
Major documentation updates
Rename PomaSummarizedExperiment to PomaCreateObject
Auto-recognition of variable types and automatic variable re-labeling in PomaCreateObject
Available violin plots with PomaBoxplots
New functions PomaPCA and PomaPLS as stand-alone functions from the old PomaMultivariate (deprecated)
Other new functions: PomaLM, PomaLMM
Post-hoc pairwise comparisons in PomaUnivariate
Update tests and vignettes

New biocViews and Description
Call external packages within each POMA function for consistency
New methods: UMAP, PCR (Principal Components Regression), RNA-seq analysis (via DESeq2 package)
Add different statistical methods in PomaVolcano()
Estimate relative quality weights in PomaLimma()
Update tests
Update vignettes
Several bug fixes

MSnbase::MSnSet class has been replaced by the SummarizedExperiment class
Color scale for all plots set to viridis (without yellow)
All output tables provided as tibble instead of matrix or data.frame
Allow users to select specific covariates and their position (importance) in the model for PomaLimma, PomaUnivariate(method = "anova"), and PomaOddsRatio
Add SD to PomaUnivariate output tables
Reduce dependencies
Update vignettes
Update documentation
Some other major and minor improvements
Some minor bugs and typos fixed
New "loading plot" in PCA
Compute p-values and FDR in PomaCorr

Remove reshape2 and Biobase packages from Imports
Implement viridis palette for PomaBoxplots, PomaDensity, and PomaMultivariate
Update mixOmics output names in PomaMultivariate
New package description and biocViews
Bug fixed in PomaMultivariate

PomaNorm and PomaImpute warnings when methos parameter is missing passed to messages
Minor bugs fixed
Minor changes in plots style
plotly package used in PomaVolcano switched to Suggests
Bioconductor badge table added to README

PomaOutliers bug fixed
New references in PomaRankProd help
PomaLimma and PomaUnivariate bug related with one covariate analysis fixed
The elbow method to calculate the optimum number of clusters has been added in PomaClust function