Changelog

Source: NEWS.md

RGenEDA 0.99.0

• Renumbered to 0.99.0 for Bioconductor submission (continues from 2.1.0).
• Added as.geneda() to build a geneda object from a SummarizedExperiment, DESeqDataSet, or DESeqTransform, carrying over counts, normalized values, colData, and optional DEG tables. Normalized values can come from an assay, a transformed object, a matrix, or be computed with DESeq2 vst or log2 CPM.
• Added biocViews, URL, and BugReports fields to DESCRIPTION.
• Removed LazyData; load the example data with data(Snail1KO).
• Added runnable examples for all exported functions using the bundled Snail1KO data.
• Documented return values for FindHVDEGs() and the show() method.
• Replaced sapply() with vapply() and 1:n with seq_len().
• Vignette now uses accessors instead of @ slot access and reports sessionInfo().
• Restyled code to Bioconductor style (4-space indents, 80-character lines).

RGenEDA 2.1.0

• Fixed cosmetics of printing statements.
• Minor bug fixes in PCA functions and accessors.

RGenEDA 2.0.2

• Fixed bug in RunPCA() where PCs beyond 10 were named NA.
• Fixed bug in PlotScree() where PCs beyond 10 were shown as NA.

RGenEDA 2.0.1

• Added PlotScree().
• PCA utilities now generate PCs dynamically up to PC10.
• Renamed DimReduction$Loadings to DimReduction$Scores.
• Added scree plot to the vignette.

RGenEDA 2.0.0

• Added assay argument to SetDEGs(), PlotMA(), and FilterDEGs() (with saveAssay).
• Added PlotVolcano(), FindHVDEGs(), and GenSave().
• Renamed eigencorr, ordcorr, and distanceHeatmap to PlotEigenCorr(), PlotOrdCorr(), and PlotDistances().
• Replaced the pasilla demo with the Snail1 KO dataset (Maturi et al., 2018).

RGenEDA 1.0.2

• Fixed example blocks in roxygen headers.
• Addressed all R CMD check errors, warnings, and notes.

RGenEDA 1.0.1

• All heatmaps now use pheatmap.
• Fixed top-gene-loading bug in PlotEigenHeatmap().
• Added optional DEGs slot to interface with DESeq2.
• Added MA plot functionality.

RGenEDA 1.0.0

• Introduced the S4 geneda object.
• Added methods for HVG calculation and PCA storage.
• Added PCA, HVG variance, and eigenvector plots.
• Eigencorrelation plots now use the top HVGs from HVG selection/PCA.
• Added unit tests and a pasilla vignette.

RGenEDA 0.0.0.900

• Initial standalone functions: variance, PCA, Euclidean distances, and eigenvector correlations.