Changes in version 2.5.3 (2025-05-19)                  

Highlights

  - Streamlined code-base – major internal refactor for clarity, speed
    and a ~20 % smaller dependency tree.
  - Consistent, flexible visualisation API across all plotting helpers.
  - Robust unit-test suite (>250 expectations) now ships with the
    package.

New & enhanced functionality

| Area | Function(s) | What changed |
|------|-------------|--------------| | Visualisation |
ridgeEnrichment() | True gradient coloring mode for numeric color.by;
optional per-cell rugs; quantile median line; fixed grey-fill bug | | |
densityEnrichment() | accepts new rug.height; ~4× faster ranking routine
using MatrixGenerics::rowMeans2; cleaner two-panel layout via patchwork
| | | gseaEnrichment() | new rug.height; clearer legend showing ES/NES/
p; internal vectorised ES calculation | | | splitEnrichment() |
rewritten: split violins when split.by has 2 levels, dodged violins
otherwise; inline boxplots; auto Z-scaling; palette helper | | |
scatterEnrichment() | density-aware points (via ggpointdensity), hex-bin
alternative, optional Pearson/Spearman overlay, continuous or discrete
color mapping | | Dimensionality reduction | performPCA() /
pcaEnrichment() | uses irlba::prcomp_irlba() automatically for large
matrices; stores eigen-values/contribution in misc;
add.percent.contribution now always respected | | Scoring backend |
escape.matrix() / .compute_enrichment() | lazy loading of heavy
back-ends (GSVA, UCell, AUCell); unified .build_gsva_param(); drops
empty gene-sets up-front | | Normalization | performNormalization() |
chunk-wise expressed-gene scaling (memory-friendly); accepts external
scale.factor; optional signed log-transform; returns object with assay
<assay>_normalized | | Gene-set retrieval | getGeneSets() | downloads
now cached under tools::R_user_dir("escape", "cache"); graceful KEGG
append; clearer error for non-human/mouse requests |

Performance & dependency reductions

  - Replaced plyr, stringr, rlang usage with base-R helpers; these
    packages are now Suggests only.
  - Common color and label utilities (.colorizer(), .colorby(),
    .orderFunction()) removed redundant tidyverse imports.
  - Internal matrices split/chunked with new .split_* helpers to cap
    memory during parallel scoring/normalization.

Bug fixes

  - Gradient mode in ridgeEnrichment() no longer produces grey fills
    when the chosen gene-set is mapped to color.by.
  - pcaEnrichment() axis labels correctly include variance contribution
    when display.factors = FALSE.
  - .grabDimRed() handles both Seurat v5 and <v5 slot structures; fixes
    missing eigen-values for SCE objects.
  - escape.matrix() respects min.size = NULL (no filtering) and handles
    zero-overlap gene-sets gracefully.
  - Global variable declarations consolidated – eliminates R CMD check
    NOTES regarding na.omit, value, etc.

Documentation

  - DESCRIPTION rewritten – heavy packages moved to Suggests; added
    explicit Config/reticulate for BiocParallel.
  - escape.gene.sets data object now fully documented with source,
    usage, and reference.

                 Changes in version 2.4.1 (2025-03-05)                  

  - Version bump to align with Bioconductor release cycle.
  - escape.matrix() now silently removes gene-sets with zero detected
    features.

                 Changes in version 2.2.4 (2025-01-13)                  

Underlying changes

  - Switched MSigDB dependency from msigdbr ➜ msigdb.
  - getGeneSets() gains local caching; supports only Homo sapiens / Mus
    musculus.

                 Changes in version 2.2.3 (2024-12-15)                  

  - Fixed groups parameter handling and data splitting in
    escape.matrix().
  - Improved efficiency of internal .split_data.matrix().

                 Changes in version 2.2.2 (2024-11-30)                  

  - Patched performNormalization() conditional logic and per-gene-set
    rescaling.

                 Changes in version 2.2.1 (2024-11-18)                  

  - Version bump for Bioconductor.

                 Changes in version 2.1.5 (2024-10-23)                  

  - Seurat v5 compatibility; mean/median options for
    heatmapEnrichment().

                 Changes in version 2.1.4 (2024-09-13)                  

  - update densityEnrichment() GSVA function pull

                 Changes in version 2.1.3 (2024-09-13)                  

UNDERLYING CHANGES

  - update densityEnrichment() for new GSVA function name
  - Parallelization of performNormalization()
  - Refactor of getGeneSets() to prevent issues with m_df error.

                 Changes in version 2.0.1 (2024-07-26)                  

UNDERLYING CHANGES

  - fixed performNormalziation() errors when input.data was a matrix,
    now requires single-cell object and enrichment data
  - passing parallel processing properly to runEscape() function.

                 Changes in version 1.99.1 (2024-02-29)                 

UNDERLYING CHANGES

  - ordering by mean values no longer changes the color order
  - add explicit BPPARAM argument to runEscape() and escape.matrix()
  - added additional details in runEscape() and escape.matrix() for
    make.positive.
  - removed plotting of splitEnrichment() for group.by = NULL
  - separated AUC calculation to rankings and AUC, this was only method
    found to get consistent scores.

                 Changes in version 1.99.0 (2024-02-27)                 

NEW FEATURES

  - Added runEscape()
  - Added geyserEnrichment()
  - Added scatterEnrichment()
  - Added heatmapEnrichment()
  - Changed enrichIt to escape.matrix()
  - Changed enrichmentPlot to densityEnrichment()
  - performPCA() now works with a matrix or single-cell object
  - pcaEnrichment() combines biplot-like functions

UNDERLYING CHANGES

  - Updated interaction with gsva package
  - Added support for GSVA calculation
  - Added support for AUCell calculation
  - Added support of visualizations and calculations for single-cell
    objects
  - Modified getGeneSets() to output a list of gene set objects with
    reformatted names following the Seurat "-" convention

DEPRECATED AND DEFUNCT

  - Deprecate getSignificance()
  - Deprecate masterPCAPlot()

                        Changes in version 1.9.0                        

  - Releveling version for commit to new Bioconductor release
  - Removed UCell internal functions to just import the Bioconductor
    UCell package

                        Changes in version 1.4.2                        

  - Fixed masterPCAPlot top_n() call to slice_max by top.contributions.

                        Changes in version 1.4.1                        

  - Version number and small edits for bioconductor compliance
  - Removed singscore method
  - Added UCell functions internally so they are compatible with
    Bioconductor
  - Fixed performPCA, eliminated merge call.

                        Changes in version 1.3.4                        

  - Normalization for ssGSEA no longer uses the range of all gene sets,
    but columns, normalizing it to 0 to 1.
  - Added Kruskal-Wallis test for additional support of multi-group
    comparison

                        Changes in version 1.3.3                        

  - Added wilcoxon and LR for getSignificance
  - median calculated and appended to the getSignificance() function
    output
  - ANOVA in getSignificance() returns p-values for each comparison
    using TukeyHSD()
  - new parameter gene.sets getSignificance() to select only gene sets
    or subsets.
  - enrichmentPlot() beta release
  - Added subcategory to getGeneSets to select subsets of libraries.
  - Added default coloring to enrichmentPlot()
  - enrichmentPlot() now imports calculations partially from GSVA
    internal functions to facilitate use of C
  - Filtering based on min.size now works instead of not working.

                        Changes in version 1.3.2                        

  - Added removal of gene sets with less than x features parameter in
    enrichIt - min.size
  - Added UCell and singScore support
  - new parameter gene.sets in MasterPCAPlot() and performPCA() to allow
    for selecting specific columns and prevent using other numeric
    vectors in meta data.

                        Changes in version 1.3.1                        

  - Aligning versions to the current bioconductor release
  - Added DietSeurat() call in vignette to prevent issues
  - Adding internal gene sets - escape.gene.sets
  - Removed lm.fit using limma from getSignificance

                        Changes in version 1.0.1                        

  - Removed ggrepel, rlang, and factoextra dependencies.
  - Updated Seurat package switch
  - Switch the way counts are processed by first eliminating rows with 0
    expression in the sparse matrix before converting to a full matrix

                       Changes in version 0.99.9                        

  - Changing Seurat dependency, updated vignette

                       Changes in version 0.99.8                        

  - Edited getSignificance ANOVA model call

                       Changes in version 0.99.7                        

  - Edited getSignificance fit call to match documentation

                       Changes in version 0.99.6                        

  - Edited match.args() in getSignificance

                       Changes in version 0.99.5                        

  - Edited match.args() in getSignificance

                       Changes in version 0.99.4                        

  - Added match.args() to getSignificance
  - Changed stop() to message()
  - Modified getSignficance to allow for ANOVA and T.test

                       Changes in version 0.99.3                        

  - Updated link in description of getGeneSets.

                       Changes in version 0.99.2                        

*Fixed a parenthesis, yeah a parenthesis. (In enrichIt() call I edited
for 99.1)

                       Changes in version 0.99.1                        

  - Removed parallel call in gsva() and added biocparallel
  - Changed cores = 4 to cores = 2 in the vignette

                       Changes in version 0.99.0                        

  - Preparing for bioconductor submission