NEWS

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scMAGeCK 0.99.1

• BiocCheck cleanup for Bioconductor review: runnable examples added to guidematrix_to_triplet, scmageck_best_lambda and scmageck_eff_estimate; \value sections added to assign_cell_identity, featurePlot, selectPlot; 1:n replaced with seq_len()/seq_along(); biocViews: Sequencing added; expanded package Description; vignette chunk labels + sessionInfo().

scMAGeCK 0.99.0

• Full compatibility with Seurat v5 / SeuratObject >= 5.
  • Seurat objects are updated with UpdateSeuratObject() on read, so objects saved by older Seurat versions no longer error with no slot of name "images".
  • Replaced the defunct slot= argument of GetAssayData() and FetchData() with layer= (defunct in SeuratObject >= 5.4).
  • The bundled example object is now stored in the Seurat v5 format.
• DESCRIPTION now requires Seurat (>= 5.0.0).
• Compiled code (RRA) now writes diagnostics to the R console via Rcpp::Rcout/Rcpp::Rcerr/Rprintf instead of std::cout/printf.
• R CMD check / BiocCheck clean-up (dead code, namespace, docs, examples).
• Version reset to 0.99.0 for Bioconductor resubmission.