Package: gedi2 Type: Package Title: Gene Expression Decomposition and Integration Version: 2.3.6 Date: 2026-10-02 Authors@R: c( person("Arsham", "Mikaeili Namini", email = "arsham.mikaeilinamini@mail.mcgill.ca", role = c("aut", "cre")), person("Hamed", "S.Najafabadi", email = "hamed.najafabadi@mcgill.ca", role = c("aut")) ) Description: 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. The method is described in Mikaeili Namini et al. (2026) , building on the original 'GEDI' model of Madrigal et al. (2024) . License: MIT + file LICENSE URL: https://github.com/csglab/gedi2 BugReports: https://github.com/csglab/gedi2/issues 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) Config/testthat/edition: 3 SystemRequirements: GNU make Encoding: UTF-8 RoxygenNote: 7.3.3 Roxygen: list(markdown = TRUE) Config/pak/sysreqs: make Repository: https://csglab.r-universe.dev Date/Publication: 2026-10-05 09:26:31 UTC RemoteUrl: https://github.com/csglab/gedi2 RemoteRef: HEAD RemoteSha: bc3b06335d304c31c09b0e52856b43cb0b3fbef5 NeedsCompilation: yes Packaged: 2026-10-05 16:33:34 UTC; root Author: Arsham Mikaeili Namini [aut, cre], Hamed S.Najafabadi [aut] Maintainer: Arsham Mikaeili Namini