NEWS
POMA 1.17.5
- Allow grouping variable selection in
PomaImpute
- New documentation
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MSnbase::MSnSet class has been replaced by the SummarizedExperiment class- Color scale for all plots set to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