NEWS

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gedi2 2.3.1

CRAN Compliance

• Replace all cat() / print() calls with message() or warning() for suppressible console output.
• Add verbose parameters to seurat_to_gedi(), gedi_to_seurat(), check_optional_dependencies(), and install_optional_dependencies().
• Replace cat()-based progress bars with txtProgressBar() across imputation and training routines.
• Replace installed.packages() with requireNamespace() for dependency checking.
• Move hdf5r from Imports to Suggests (optional dependency for H5AD I/O).
• Add ggplot2 and scales to Imports; add uwot and digest to Suggests.
• Use CRAN-required two-line LICENSE format.
• Add @return documentation tags to all exported and documented functions.
• Replace non-ASCII characters in C++ source files with ASCII equivalents.
• Remove redundant Maintainer field from DESCRIPTION.

gedi2 2.3.0

• Initial public release with C++ backend and R6 interface.
• Support for multiple data modalities (count matrices, paired data, binary indicators).
• Latent variable model with block coordinate descent optimization.
• Dimensionality reduction, batch correction, and imputation.
• Differential expression and pathway association analysis.
• H5AD file I/O for Python interoperability.
• Seurat and SingleCellExperiment integration.