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POMA 1.15.17

  • Analyzing data with random effects in PomaLimma
  • Select outcome factor in PomaBoxplots, PomaDensity, and PomaOutliers
  • Documentation improvements
  • Introduces PomaEnrichment for gene set analysis
  • Allows custom study designs in PomaDESeq

POMA 1.14.0

  • Released to Bioconductor 3.19

POMA 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

POMA 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

POMA 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  • MSnbase::MSnSet class has been replaced by the SummarizedExperiment class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

POMA 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

POMA 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

POMA 1.0.0

  • Released to Bioconductor 3.12

POMA 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

POMA 0.99.37

  • POMA has been accepted to Bioconductor!
  • PomaRankProd minor bug fixed
  • Authors updated
  • Bioconductor logo

POMA 0.99.33

  • All Bioconductor issues in the review process have been addressed
  • POMA EDA vignette added

POMA 0.99.16

  • BiocCeck requirements fixed
  • Examples added in functions
  • pkgdown files removed from master branch

POMA 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