NEWS.md

2.5.5 (2025-06-11)

Bug fix & enhanced functionality

2.5.4 (2025-06-05)

Bug fixes

2.5.3 (2025-05-19)

Highlights

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

Bug fixes

Documentation

2.4.1 (2025-03-05)

2.2.4 (2025-01-13)

Underlying changes

2.2.3 (2024-12-15)

2.2.2 (2024-11-30)

2.2.1 (2024-11-18)

2.1.5 (2024-10-23)

2.1.4 (2024-09-13)

2.1.3 (2024-09-13)

UNDERLYING CHANGES

2.0.1 (2024-07-26)

UNDERLYING CHANGES

1.99.1 (2024-02-29)

UNDERLYING CHANGES

1.99.0 (2024-02-27)

NEW FEATURES

UNDERLYING CHANGES

DEPRECATED AND DEFUNCT

CHANGES IN VERSION 1.9.0

CHANGES IN VERSION 1.4.2

CHANGES IN VERSION 1.4.1

CHANGES IN VERSION 1.3.4

CHANGES IN VERSION 1.3.3

CHANGES IN VERSION 1.3.2

CHANGES IN VERSION 1.3.1

CHANGES IN VERSION 1.0.1

CHANGES IN VERSION 0.99.9

CHANGES IN VERSION 0.99.8

CHANGES IN VERSION 0.99.7

CHANGES IN VERSION 0.99.6

CHANGES IN VERSION 0.99.5

CHANGES IN VERSION 0.99.4

CHANGES IN VERSION 0.99.3

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

CHANGES IN VERSION 0.99.0



ncborcherding/escape documentation built on June 12, 2025, 1 p.m.