Release Notes

20250124 - v0.0.2.0

Major Release - Bug Fixes and Improvements

Breaking Changes: - Removed dependency on ggtree (use ape instead) - Migrated from easyLift (GitHub) to easylift (Bioconductor) - Updated for Seurat v5 compatibility

Bug Fixes: - Fixed parse error with ref_genome parameter (Issue #15) - Fixed hardcoded hg19 in EpiTraceAge_Convergence (Issue #12) - Added offline mode support for UCSC chromosome download (Issue #3) - Fixed vector mismatch warning in age calculation (Issue #19) - Fixed final_cells undefined bug when run_reduction=FALSE

New Features: - Added comprehensive documentation on bulk vs single-cell age interpretation (Issue #13) - Added documentation explaining clock reference options (Issue #17)

Dependencies Updated: - Removed: ggtree, easyLift - Added: easylift (Bioconductor) - Updated: Seurat v5 API compatibility (slot → layer)

Notes: - All 9 fixes tested with bulk ATAC demo data (120 cells) - EpiTrace now works offline without UCSC access - Compatible with Bioconductor easylift for genome liftover

20240127

Updated readthedocs introduction.

Removed unused dependencies for now.

20231011

Included G-quadruplex reference set:

G-quadruplex (G4) harboring sites (pGQS) are provided for human (hg19), mouse (mm10), zebrafish (drerio10), fly (dm6), nematode (ce11) and yeast (sc3) genomes. Source of G4 regions: GSE110582 (mm10, dm6, ce11, sc3), GSE187007 (hg19), or G4Hunter prediction (drerio10).

G4Hunter source: https://github.com/LacroixLaurent/G4HunterPaperGit

20221008

Added frequently used non-human clockDML-like genomic regions as reference set for EpiTrace inference in: Drosophila, Zebrafish, and Mouse.

20220910

Added mouse ClockDML sites (from Zhou et al 2022, PMID 35873672) for mouse single cell EpiTrace inference.

20220611

Added .rds files similar to the clock_gr_list data (for external loading).

Added %ni% function (taken from ArchR).

20220510

First initialize version