NEWS

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gedi2 2.3.6 (2026-10-05)

Maintenance

• Compatibility with Eigen 5.0 (upcoming RcppEigen 0.4.x). Eigen 5.0 removes Eigen::MappedSparseMatrix, so the sparse-matrix helpers compute_Yp(), compute_Mp(), compute_s_0(), compute_o_0() and eigenSparseMatVecProduct() now take Eigen::Map<Eigen::SparseMatrix<double>> instead. The package still builds against the current CRAN RcppEigen (0.3.4.0.2) and the RcppEigen release candidate (0.4.9.9-2). No user-visible changes. Contributed by Dirk Eddelbuettel (@eddelbuettel) in #28; see RcppCore/RcppEigen#151 for the wider Eigen 5.0 migration.

gedi2 2.3.5

New features

• plot_features() gains two differential projection types (#26):
  • projection = "diffexp" plots the per-cell differential expression for selected genes, given a contrast (optionally adding the global offset via include_O = TRUE). The full J x N matrix is never materialised.
  • projection = "diffadb" plots the per-cell differential pathway activity for selected pathways (requires a gene-level prior C).
• New method model$diffADB(contrast) returns the differential pathway activity (num_pathways x N). It is the exact differential of ADB (i.e. ADB(Z + dQ) - ADB(Z)), applying the same solve_A shrinkage so it stays on the same scale as model$projections$ADB.

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.