NEWS.md

In pcastellanoescuder/POMA_package: Tools for Omics Data Analysis

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• MSnbase::MSnSet class has been replaced by the SummarizedExperiment class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

pcastellanoescuder/POMA_package documentation built on Oct. 13, 2024, 8:47 p.m.