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 |
| Reference manual: | gedi2.html , gedi2.pdf |
| 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 |
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