gedi2: Gene Expression Decomposition and Integration

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>.

Version:	2.3.4
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)
Published:	2026-05-19
DOI:	10.32614/CRAN.package.gedi2 (may not be active yet)
Author:	Arsham Mikaeili Namini [aut, cre], Hamed S.Najafabadi [aut]
Maintainer:	Arsham Mikaeili Namini <arsham.mikaeilinamini at mail.mcgill.ca>
BugReports:	https://github.com/csglab/gedi2/issues
License:	MIT + file LICENSE
URL:	https://github.com/csglab/gedi2
NeedsCompilation:	yes
SystemRequirements:	GNU make
Materials:	NEWS
CRAN checks:	gedi2 results

Documentation:

Reference manual:

gedi2.html , gedi2.pdf

Downloads:

Package source:	gedi2_2.3.4.tar.gz
Windows binaries:	r-devel: not available, r-release: gedi2_2.3.4.zip, r-oldrel: gedi2_2.3.4.zip
macOS binaries:	r-release (arm64): gedi2_2.3.4.tgz, r-oldrel (arm64): gedi2_2.3.4.tgz, r-release (x86_64): gedi2_2.3.4.tgz, r-oldrel (x86_64): gedi2_2.3.4.tgz

Linking:

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