R Observatory: Metrics for grandR version 0.2.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

grandR

0.2.7

Comprehensive Analysis of Nucleotide Conversion Sequencing Data

1packages depend

3.9Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Florian ErhardFirst published 2022-09-206 releasesCRAN page ↗GitHub ↗

Nucleotide conversion sequencing experiments have been developed to add a temporal dimension to RNA-seq and single-cell RNA-seq. Such experiments require specialized tools for primary processing such as GRAND-SLAM, (see 'Jürges et al' doi:10.1093/bioinformatics/bty256) and specialized tools for downstream analyses. 'grandR' provides a comprehensive toolbox for quality control, kinetic modeling, differential gene expression analysis and visualization of such data. Fast Wilcoxon tests are supported via the 'presto' package (available at https://github.com/immunogenomics/presto).

Install

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

install.packages("grandR", 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("erhard-lab/grandR")

Development version from erhard-lab/grandR. 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-grandr

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-grandR

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-grandR

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

Health

CRAN checks

13OK

Slowest check: 4.8 min · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

19

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
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 323 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 93%
Documented parameters: 97%
Return-value docs: 98%
References docs: 0%

Downloads

3.9K

CRAN downloads in the past year

Rank #10,988 · ~11/day · ~323/mo

Releases R versions

Daily download trend is not available in this view yet.

22930 days

88490 days

3.9K1 year

Compare downloads with other packages →

Also on463 r2u21 autocran

Repository

GitHub ↗ erhard-lab/grandr

17Stars

4Forks

7Open issues

0Open PRs

6Releases

324Commits

21Contributors

324 commits · Last activity 2026-01-13 · 0% stars, 30d

Stars over time

2025-08-14 · 152026-07-07 · 17

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/erhard-lab/grandr on 2026-08-16.

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

41 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (19)

statsMatrixrlang ggplot2grDevicespatchwork RCurl plyrparallelreshape2MASSscales cowplot minpack.lm lfc labelingmethodsutilsnumDeriv

LinkingTo (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

HetSeq

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Florian Erhard

Author, Maintainer

Authors (1)

Florian Erhard

Author, Maintainer

Contributors (2)

Teresa Rummel

Contributor

Julian Selke

Contributor · added in 0.2.7

Listed in earlier versions (2)

Lygeri Sakellaridi

no longer listed · 0.2.0 to 0.2.6

Kevin Berg

no longer listed · 0.2.5 to 0.2.6

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.2.7Latest
2026-01-14 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
0.2.6
2025-01-22 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.2.5
2024-02-15 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.2.2
2023-04-20 · diff ↗
0.2.1
2023-02-27 · diff ↗
0.2.0
2022-09-20
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-09-20
Total releases: 6 / 4 yrs
License: Apache License (>= 2)
Minimum R: ≥ 3.5.0
Download size: 646 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("grandR")

Format

Erhard, F., Rummel, T., & Selke, J. (2026). grandR: Comprehensive Analysis of Nucleotide Conversion Sequencing Data (Version 0.2.7) [Computer software]. https://doi.org/10.32614/CRAN.package.grandR

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 grandR version 0.2.7 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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