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gedi2  

Gene Expression Decomposition and Integration
View on CRAN: Click here


Download and install gedi2 package within the R console
Install from CRAN:
install.packages("gedi2")

Install from Github:
library("remotes")
install_github("cran/gedi2")

Install by package version:
library("remotes")
install_version("gedi2", "2.3.4")



Attach the package and use:
library("gedi2")
Maintained by
Arsham Mikaeili Namini
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2026-05-19
Latest Update: 2026-05-19
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>.
How to cite:
Arsham Mikaeili Namini (2026). gedi2: Gene Expression Decomposition and Integration. R package version 2.3.4, https://cran.r-project.org/web/packages/gedi2. Accessed 08 Oct. 2026.
Previous versions and publish date:
(2026-10-05 11:50), 2.3.4 (2026-05-19 09:30)
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Complete documentation for gedi2
Functions, R codes and Examples using the gedi2 R package
Full gedi2 package functions and examples
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