Changes in version 1.13.26 - 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 Changes in version 1.7.19 - 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PomaLimma() - Update tests - Update vignettes - Several bug fixes Changes in version 1.5.16 - MSnbase::MSnSet class has been replaced by the SummarizedExperiment class - Color scale for all plots set to viridis (without yellow) - All output tables provided as tibble instead of matrix or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 Changes in version 1.1.15 - 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 Changes in version 1.1.8 - 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 Changes in version 1.0.0 - Released to Bioconductor 3.12 Changes in version 0.99.45 - 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 Changes in version 0.99.37 - POMA has been accepted to Bioconductor! - PomaRankProd minor bug fixed - Authors updated - Bioconductor logo Changes in version 0.99.33 - All Bioconductor issues in the review process have been addressed - POMA EDA vignette added Changes in version 0.99.16 - BiocCeck requirements fixed - Examples added in functions - pkgdown files removed from master branch Changes in version 0.99.0 - POMA is now submitted to Bioconductor! - All features implemented work as expected - All tests finished - Achieved desired coverage (>95%) - Vignettes and documentation are ready for the first release