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:
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