NEWS

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cellchatr 0.99.1

Bioconductor review changes

• Added Bioconductor-interoperable API:
  • findOverexpressedGenes() S4 generic with methods for matrices (dense or sparse) and SummarizedExperiment / SingleCellExperiment objects (assay.type and a colData column for cell labels).
  • matchLRPairs() returns matching interactions as an S4Vectors::DataFrame.
  • identifyInteractions() runs the full workflow in one call.
• Removed the hello_world() scaffold function.
• rust_wilcoxon_filter() now computes a one-sided ("greater") p-value, as documented; previously it was two-sided and also reported under-expressed genes.
• rust_wilcoxon_filter() and rust_match_lr_pairs() now raise an R error for inputs of mismatched lengths instead of panicking.
• CellChat is no longer referred to as a dependency: any ligand-receptor table can be used, and the CellChatDB interaction table is supported directly.

cellchatr 0.99.0

• Initial Bioconductor submission.
• rust_subset_genes(), rust_wilcoxon_filter() and rust_match_lr_pairs() implemented in Rust.