grandR

0.2.7

Comprehensive Analysis of Nucleotide Conversion Sequencing Data

1packages depend

4Kdownloads / 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: 5.8 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Yes

Vignettes

Yes

README

Dependencies · direct

Check history

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

Downloads

CRAN downloads in the past year

Rank #11,274 · ~11/day · ~333/mo

grandR Releases R versions

Daily download trend is not available in this view yet.

42930 days

94890 days

4K1 year

Compare downloads with other packages →

Also on475 r2u13 autocran

Repository

GitHub ↗ erhard-lab/grandr

17Stars

4Forks

7Open issues

0Open PRs

6Releases

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

Code Composition

R 12,089 (64%)Rd 6,389 (34%)C 317 (2%)Vignettes 73 (0%)

Code characteristics

Object systems

S316

Cyclomatic complexity: 3.0 median / 105 max
Documented parameters: 97%

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

300 165 exported

Complexity

6.1 avg / 105 max

Call network

300 nodes / 626 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Call graph

Open call graph →

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Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (3)

Maintainer (1)

Florian Erhard

Author, Maintainer

Authors (1)

Florian Erhard

Author, Maintainer

Contributors (2)

Teresa Rummel

Contributor

Julian Selke

Contributor

Release 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