Package: gedi2
Type: Package
Title: Gene Expression Decomposition and Integration
Version: 2.3.4
Date: 2026-05-09
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. Core algorithms are described in 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: 2026-05-13 17:32:10 UTC; arsham79
Author: Arsham Mikaeili Namini [aut, cre],
  Hamed S.Najafabadi [aut]
Maintainer: Arsham Mikaeili Namini <arsham.mikaeilinamini@mail.mcgill.ca>
Repository: CRAN
Date/Publication: 2026-05-19 07:30:21 UTC
Built: R 4.5.2; x86_64-apple-darwin20; 2026-05-19 09:49:06 UTC; unix
Archs: gedi2.so.dSYM
