R Observatory: Metrics for SRscore version 0.1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SRscore

0.1.2

Simple Transcriptome Meta-Analysis for Identifying Stress-Responsive Genes

0packages depend

3.4Kdownloads / year

63.7%test coverage

13/13checks pass

Overview

About

Maintained by Yusuke FukudaFirst published 2026-01-081 releasesCRAN page ↗

Stress Response score (SRscore) is a stress responsiveness measure for transcriptome datasets and is based on the vote-counting method. The SRscore is determined to evaluate and score genes on the basis of the consistency of the direction of their regulation (Up-regulation, Down-regulation, or No change) under stress conditions across multiple analyzed research projects. This package is based on the HN-score (score based on the ratio of gene expression between hypoxic and normoxic conditions) proposed by Tamura and Bono (2022) doi:10.3390/life12071079, and can calculate both the original method and an extended calculation method described in Fukuda et al. (2025) doi:10.1093/plphys/kiaf105.

Install

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

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

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

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-srscore

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-SRscore

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-SRscore

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

Health

CRAN checks

13OK

Slowest check: 1.7 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.05

63.7%

Coverage · measured lines

100%

Documentation · exports

4

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
OK2026-06-27
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-21
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 3 earlier snapshots

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
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 317 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

3.4K

CRAN downloads in the past year

Rank #8,367 · ~9/day · ~284/mo

Releases R versions

Daily download trend is not available in this view yet.

28430 days

1.1K90 days

3.4K1 year

Compare downloads with other packages →

Also on51 r2u22 autocran

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (4)

dplyr tidyrutilsrlang

LinkingTo (0)

none

Suggests (12)

knitr rmarkdown testthat ggplot2 tibble ComplexHeatmap clusterProfiler org.At.tair.db BiocStyle RColorBrewer genefilter DT

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Yusuke Fukuda

Author, Maintainer

Authors (2)

Yusuke Fukuda

Author, Maintainer

Atsushi Fukushima

Author

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.2Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-01-08
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Bundled data: 795 KB / 10 files
Download size: 2.0 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SRscore")

Format

Fukuda, Y., & Fukushima, A. (2026). SRscore: Simple Transcriptome Meta-Analysis for Identifying Stress-Responsive Genes (Version 0.1.2) [Computer software]. https://doi.org/10.32614/CRAN.package.SRscore

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 SRscore version 0.1.2 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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