R Observatory: Metrics for ReporterScore version 0.2.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ReporterScore

0.2.5Package record

Generalized Reporter Score-Based Enrichment Analysis for Omics Data

0packages depend

3.6Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Chen PengCRAN page ↗GitHub ↗Issues ↗

Inspired by the classic 'RSA', we developed the improved 'Generalized Reporter Score-based Analysis (GRSA)' method, implemented in the R package 'ReporterScore', along with comprehensive visualization methods and pathway databases. 'GRSA' is a threshold-free method that works well with all types of biomedical features, such as genes, chemical compounds, and microbial species. Importantly, the 'GRSA' supports multi-group and longitudinal experimental designs, because of the included multi-group-compatible statistical methods.

Changes in 0.2.5

Others

move calculate_NS, update_all_pathway_NS, calculate_ZN_score function to a new package TWICE <2026-02-20, Fri>

From NEWS.md in the release

Install

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

install.packages("ReporterScore", 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("Asa12138/ReporterScore")

Development version from Asa12138/ReporterScore. 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-reporterscore

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-ReporterScore

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-ReporterScore

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

CRAN check page ↗

Slowest check: 3.3 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-25

Show 1 earlier changeHide 1 earlier change

NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.2.5

README· In the repository, left out of the releaseVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.2.5Citation fileYes · cites a publication

Help pages: 67 (2 internal)includes a package overview page
Examples that run: 50%15 run in a plain check (1 of them under a condition) · 15 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 60%
Documented parameters: 98%
Return-value docs: 100%
Help pages citing references: 3%

Vignettes (1)

ReporterScore HTML

How these are measured

Downloads

3.6K

CRAN downloads in the past year

Rank #10,690 · ~10/day · ~299/mo

Releases R versions

Daily download trend is not available in this view yet.

39130 days

95090 days

3.6K1 year

Compare downloads with other packages →

Also on127 r2u3 autocran

How downloads are counted

Repository

asa12138/reporterscore ↗Account: Asa12138

88Stars

10Forks

1Open issues

2Open PRs

0Releases

87Commits

1Commit identities

87 commits · Last activity 2026-04-28 · 0% stars, 30d · Default branch at 0.2.6, ahead of CRAN 0.2.5 (checked 2026-10-11)

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 5
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2025-08-19 · 752026-07-07 · 88

How these are measured

PracticesBeta

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

Checks run against github.com/asa12138/reporterscore on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-04-28 · The repository has a site deploy workflow

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

Dependencies

Declared dependencies

34 external dependencies (excludes base and recommended)

Installing ReporterScore adds 37 packages (19 with compiled code, 33 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, Rcpp 1.8 MB.

Depends (1)

R >= 4.2.0

Imports (12)

magrittr dplyrstatsggplot2 pcutils (>= 0.2.5)utilsscales ggnewscale ggrepel reshape2 stringr foreach

LinkingTo (0)

none

Suggests (24)

knitr rmarkdown plyr e1071 factoextra snow doSNOW pheatmap readr R.utils KEGGREST ggkegg clusterProfiler enrichplot pathview GSA vegan MetaNet igraph ggraph PADOG safe rSEA GSVA

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Chen Peng

Author, Maintainer since 0.1.1 (2024)

Releases (9)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.2.5Latest
record
2026-02-20 · current release · diff ↗ ·
added 11 exports
c_net_from_pathway_xml, get_all_pathway_net_index, load_CAZy_info, load_Enzyme_htable, load_Enzyme_info, load_pathway_xml_ls, pathway_net_index, plot_pathway_net, update_CAZy_info, update_Enzyme_info, update_pathway_xml_ls
R
R 4.5.0 released · 2025-04-11
0.1.9
record
2024-11-28 · diff ↗
0.1.8
record
2024-08-26 · diff ↗
0.1.7
record
2024-08-21 · diff ↗ ·
added 1 export
export_report_table
0.1.6
record
2024-06-25 · diff ↗
0.1.5
record
2024-06-05 · diff ↗ ·
added 1 export
combine_rs_res
R
R 4.4.0 released · 2024-04-24
unarchivedReturned to CRAN
2024-03-29
0.1.4
record
2024-03-29 · diff ↗ ·
added 4 exports
KO_gsva, KO_padog, KO_safe, KO_sea
archivedRemoved from CRAN
2024-03-10
issues were not corrected in time
0.1.2
record
2024-01-15 · diff ↗ ·
added 2 exports
plot_KOs_network, plot_features_network
0.1.1
record
2024-01-12
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-01-12
Total releases: 9 / 2 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.2.0
Bundled data: 3.2 MB / 12 files
Download size: 3.3 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("ReporterScore")

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

It points to 10.1093/bib/bbae116.

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 ReporterScore version 0.2.5 [Data set]. HJJB, LLC. Data release v2026-10-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →