Gene Expression Decomposition and Integration R package gedi2 version 2.3.4 A memory-efficient implementation for integrating gene expression data from single-cell RNA sequencing experiments. Uses a C++ backend with thin R wrappers to enable analysis of large-scale single-cell datasets. The package supports multiple data modalities including count matrices, paired data (splicing, RNA velocity, CITE-seq), and binary indicators. It implements a latent variable model with block coordinate descent optimization for dimensionality reduction and batch effect correction. Core algorithms are described in Madrigal et al. (2024) <doi:10.1038/s41467-024-50963-0>. Software Depends: R (>= 4.0.0) Imports: Rcpp (>= 1.0.0), R6 (>= 2.5.0), Matrix (>= 1.3.0), ggplot2, scales, methods, stats, utils LinkingTo: Rcpp, RcppEigen Suggests: hdf5r, uwot, digest, glmnet, Seurat, SeuratObject, SingleCellExperiment, testthat (>= 3.0.0) Arsham Mikaeili Namini <arsham.mikaeilinamini@mail.mcgill.ca> Comprehensive R Archive Network (CRAN) Arsham Mikaeili Namini [aut, cre], Hamed S.Najafabadi [aut] MIT + file LICENSE (https://CRAN.R-project.org/package=gedi2/LICENSE) 2026-05-19 application/tgz https://CRAN.R-project.org/package=gedi2 doi:10.32614/CRAN.package.gedi2