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) <doi:10.1093/bioinformatics/btag334>, building on
        the original GEDI model of Madrigal et al. (2024)
        <doi:10.1038/s41467-024-50963-0>.
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
NeedsCompilation: yes
Packaged: 2026-10-05 16:28:39 UTC; root
Author: Arsham Mikaeili Namini [aut, cre], Hamed S.Najafabadi [aut]
Maintainer: Arsham Mikaeili Namini
 <arsham.mikaeilinamini@mail.mcgill.ca>
Config/pak/sysreqs: make
Repository: https://cran.r-universe.dev
Date/Publication: 2026-10-05 16:12:37 UTC
RemoteUrl: https://github.com/cran/gedi2
RemoteRef: HEAD
RemoteSha: 46960b8cd320135ac81f0a9f2c936323dd9e3e5d