R Observatory: Metrics for nebula version 1.5.8

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

nebula

1.5.8

Negative Binomial Mixed Models Using Large-Sample Approximation for Differential Expression Analysis of ScRNA-Seq Data

0packages depend

6.8Kdownloads / year

2.8%test coverage

13/13checks pass

Overview

About

Maintained by Liang HeFirst published 2022-01-216 releasesCRAN page ↗GitHub ↗

A fast negative binomial mixed model for conducting association analysis of multi-subject single-cell data. It can be used for identifying marker genes, differential expression and co-expression analyses. The model includes subject-level random effects to account for the hierarchical structure in multi-subject single-cell data. See He et al. (2021) doi:10.1038/s42003-021-02146-6.

Install

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

install.packages("nebula", 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("lhe17/nebula")

Development version from lhe17/nebula. 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-nebula

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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-nebula

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-nebula

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 6.0 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.31

2.8%

Coverage · measured lines

100%

Documentation · exports

12

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-10
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 7 earlier snapshots

ERROR2026-05-03
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 3,568 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 67%
Documented parameters: 100%
Return-value docs: 100%
References docs: 14%

Downloads

6.8K

CRAN downloads in the past year

Rank #4,301 · ~19/day · ~564/mo

Releases R versions

Daily download trend is not available in this view yet.

57830 days

1.9K90 days

6.8K1 year

Compare downloads with other packages →

Also on2.7K r2u

Repository

GitHub ↗ lhe17/nebula

61Stars

8Forks

51Open issues

0Open PRs

12Releases

55Commits

2Contributors

55 commits · Last activity 2026-07-12 · +1.7% stars, 30d

Stars over time

2026-07-14 · 592026-07-21 · 61

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/lhe17/nebula on 2026-08-16.

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.4.0

Imports (12)

Rcpp nloptrstatsMatrixmethodsRfast trust parallelly doFuture future (>= 1.32.0)foreach doRNG

LinkingTo (2)

Rcpp RcppEigen

Suggests (6)

knitrutilsrmarkdown Seurat SingleCellExperiment testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Liang He

Author, Maintainer

Authors (1)

Liang He

Author, Maintainer

Contributors (1)

Raghav Sharma

Contributor · added in 1.5.3

Package Timeline

6 releases. Pick two to compare their code metrics. R releases are shown for context.

1.5.8Latest
2026-07-12 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.5.6
2025-12-07 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.5.3
2024-02-16 · diff ↗
1.4.2
2023-07-06 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.2.2
2023-01-18 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.2.0
2022-01-21
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2022-01-21
Total releases: 6 / 4 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.4.0
Bundled data: 57 KB / 1 file
Download size: 572 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("nebula")

Format

He, L., & Sharma, R. (2026). nebula: Negative Binomial Mixed Models Using Large-Sample Approximation for Differential Expression Analysis of ScRNA-Seq Data (Version 1.5.8) [Computer software]. https://doi.org/10.32614/CRAN.package.nebula

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 nebula version 1.5.8 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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