R Observatory: Metrics for gedi2 version 2.3.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

gedi2

2.3.6Package record

Gene Expression Decomposition and Integration

0packages depend

1.9Kdownloads / year

41.9%test coverage

13/13flavors OK

Overview

About

Maintained by Arsham Mikaeili NaminiCRAN page ↗GitHub ↗Issues ↗

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. The method is described in Mikaeili Namini et al. (2026) doi:10.1093/bioinformatics/btag334, building on the original GEDI model of Madrigal et al. (2024) doi:10.1038/s41467-024-50963-0.

Changes in 2.3.6

Maintenance

Compatibility with Eigen 5.0 (upcoming RcppEigen 0.4.x). Eigen 5.0 removes Eigen::MappedSparseMatrix, so the sparse-matrix helpers compute_Yp(), compute_Mp(), compute_s_0(), compute_o_0() and eigenSparseMatVecProduct() now take Eigen::Map<Eigen::SparseMatrix<double>> instead. The package still builds against the current CRAN RcppEigen (0.3.4.0.2) and the RcppEigen release candidate (0.4.9.9-2). No user-visible changes. Contributed by Dirk Eddelbuettel (@eddelbuettel) in #28; see RcppCore/RcppEigen#151 for the wider Eigen 5.0 migration.

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("gedi2", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("csglab/gedi2")

Development version from csglab/gedi2. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-gedi2

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-gedi2

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-gedi2

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 7.1 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK7 OK2026-05-20

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.3.6

README· In the repository, left out of the releaseVignettesNoNEWSYes · 100% structured · mentions 2.3.6Citation fileNo

Help pages: 28 (13 internal)includes a package overview page
Examples that run: 13%2 run in a plain check · 14 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 98%
Return-value docs: 100%
Help pages citing references: 4%

How these are measured

Downloads

1.9K

CRAN downloads in the past year

Rank #9,470 · ~5/day · ~162/mo

Releases R versions

Daily download trend is not available in this view yet.

45430 days

1K90 days

1.9K1 year

Compare downloads with other packages →

Also on85 r2u2 autocran

How downloads are counted

Repository

csglab/gedi2 ↗Organization: csglab

22Stars

1Forks

0Open issues

0Open PRs

3Releases

200Commits

3Commit identities

human-cell-atlassingle-cell-genomicssingle-cell-rna-seq

200 commits · Last activity 2026-10-05 · +340% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 94%
Median days to close, 50 most recently updated closed issues: 1
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2026-01-14 · 12026-10-04 · 22

How these are measured

PracticesBeta

5 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/csglab/gedi2 on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows

Docs source (1)

GitHub Pages site last deployed 2025-11-05

Coverage (1)

Coverage reporting

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Installing gedi2 adds 19 packages (9 with compiled code, 17 MB of source tarballs). Heaviest: ggplot2 6.0 MB, Rcpp 1.8 MB, RcppEigen 1.7 MB.

Depends (1)

R >= 4.0.0

Imports (8)

Rcpp R6Matrixggplot2 scalesmethodsstatsutils

LinkingTo (2)

Rcpp RcppEigen

Suggests (8)

hdf5r uwot digest glmnet Seurat SeuratObject SingleCellExperiment testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (2)

Arsham Mikaeili Namini

Author, Maintainer since 2.3.4 (2026)

Hamed S.Najafabadi

Author

Releases (2)

Pick two releases to compare their code metrics.

2.3.6Latest
record
2026-10-05 · current release · diff ↗
2.3.4
record
2026-05-19
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-05-19
Total releases: 2 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.0.0
Download size: 121 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("gedi2")

Format

Mikaeili Namini, A., & S.Najafabadi, H. (2026). gedi2: Gene Expression Decomposition and Integration (Version 2.3.6) [Computer software]. https://doi.org/10.32614/CRAN.package.gedi2

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for gedi2 version 2.3.6 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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