Changes in version 2.1.0                        

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

                        Changes in version 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.

                        Changes in version 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.

                        Changes in version 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).

                        Changes in version 1.0.2                        

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

                        Changes in version 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.

                        Changes in version 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.

                       Changes in version 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).

                      Changes in version 0.0.0.900                      

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