R Observatory: Metrics for grandR version 0.2.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

grandR

0.2.7Package record

Comprehensive Analysis of Nucleotide Conversion Sequencing Data

1packages depend

3.8Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Florian ErhardCRAN page ↗GitHub ↗Issues ↗

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).

Changes in 0.2.7

Major updates

Removed dependency to monocle (which caused problems on the newest cran build)
Added wilcoxon test (optionally via presto) for differential gene expression

Smaller updates

More useful parameter name count.as.integer for GetTable, GetMatrix and GetData
Expanded code for estimation in the mixture model
Removed the ComputeAbsolute function
Reading llr and shape matrices of Grand3 output

From NEWS.md in the release

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. 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-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). 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

Additional issues

rchk

CRAN check page ↗

Slowest check: 4.7 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK12 OK2026-04-25

Show 1 earlier changeHide 1 earlier change

NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.2.7

READMEYes · 323 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.2.7Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 126
Examples that run: 90%36 run in a plain check · 2 only when donttest examples are enabled (R CMD check --as-cran) · 1 never run · 1 hold no code
Exported functions with examples: 33%
Documented parameters: 97%
Return-value docs: 98%
Help pages citing references: 0%

Vignettes (1)

Getting started

How these are measured

Downloads

3.8K

CRAN downloads in the past year

Rank #10,928 · ~10/day · ~317/mo

Releases R versions

Daily download trend is not available in this view yet.

36530 days

95290 days

3.8K1 year

Compare downloads with other packages →

Also on388 r2u8 autocran

How downloads are counted

Repository

erhard-lab/grandr ↗Organization: erhard-lab

17Stars

4Forks

7Open issues

0Open PRs

6Releases

324Commits

21Commit identities

324 commits · Last activity 2026-01-13 · 0% stars, 30d · Discussions: 9 posts

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 14
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2025-08-14 · 152026-07-07 · 17

How these are measured

PracticesBeta

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

Checks run against github.com/erhard-lab/grandr on 2026-10-11.

Governance and community (1)

Issue templates

Docs source (1)

pkgdown

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

41 external dependencies (excludes base and recommended)

Installing grandR adds 30 packages (15 with compiled code, 33 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, patchwork 3.2 MB.

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

Imports 1

Depends, Imports or LinkingTo, most downloaded first

HetSeq

How these are counted

Code & Tests

Datasets

People & History

People (3)

Florian Erhard

Author, Maintainer since 0.2.0 (2022)

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

Releases (6)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.2.7Latest
record
2026-01-14 · current release · diff ↗ ·
removed 1 export
ComputeAbsolute

added 2 exports
Renamer, Wilcoxon
R
R 4.5.0 released · 2025-04-11
0.2.6
record
2025-01-22 · diff ↗ ·
added 2 exports
ComputeTotalExpression, Summarize
R
R 4.4.0 released · 2024-04-24
0.2.5
record
2024-02-15 · diff ↗ ·
added 4 exports
ComputeColumnStatistics, GetPairContrasts, PoolColumns, ReadFeatureCounts
R
R 4.3.0 released · 2023-04-21
0.2.2
record
2023-04-20 · diff ↗ ·
added 10 exports
ComputeNonConstantParam, ComputeSummaryStatistics, Correct4sUDropoutHLFactor, Correct4sUDropoutHLSpline, Estimate4sUDropoutPercentage, Estimate4sUDropoutPercentageForSample, EvaluateNonConstantParam, SimulateTimeCourseNonConstant, f.nonconst, f.nonconst.linear
0.2.1
record
2023-02-27 · diff ↗ ·
removed 8 exports
GetSparseMatrix, PlotToxicityTest, PlotToxicityTestAll, PlotToxicityTestDeferAll, PlotToxicityTestRank, PlotToxicityTestRankAll, PlotToxicityTestRankDeferAll, VersionString

added 26 exports
ComputePseudoNtr, CreatePdfs, CreatePdfsComparison, CreatePdfsParameters, CreatePdfsProfiles, DESeq2BIC, GetMatrix, IsSparse, Metadata, Pairwise, Plot4sUDropout, Plot4sUDropoutAll, Plot4sUDropoutDeferAll, Plot4sUDropoutRank, Plot4sUDropoutRankAll, Plot4sUDropoutRankDeferAll, ReadCounts, ReadNewTotal, RenameColumns, SaveNtrSlot, Semantics.concentration, SwapColumns, UpdateSymbols, UseNtrSlot, as.Seurat.grandR, merge.grandR
0.2.0
record
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

Cite

Cite this package

Run in R for the authors' entry:

citation("grandR")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1093/bioinformatics/bty256, 10.1038/s41586-019-1369-y, 10.1038/s41467-023-39163-4.

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 v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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