R Observatory: Metrics for easybio version 1.2.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

easybio

1.2.3

Comprehensive Single-Cell Annotation and Transcriptomic Analysis Toolkit

0packages depend

4.1Kdownloads / year

1.8%test coverage

13/13checks pass

Overview

About

Maintained by Wei CuiFirst published 2024-09-057 releasesCRAN page ↗GitHub ↗

Provides a comprehensive toolkit for single-cell annotation with the 'CellMarker2.0' database (see Xia Li, Peng Wang, Yunpeng Zhang (2023) <doi: 10.1093/nar/gkac947>). Streamlines biological label assignment in single-cell RNA-seq data and facilitates transcriptomic analysis, including preparation of TCGAhttps://portal.gdc.cancer.gov/ and GEOhttps://www.ncbi.nlm.nih.gov/geo/ datasets, differential expression analysis and visualization of enrichment analysis results. Additional utility functions support various bioinformatics workflows. See Wei Cui (2024) <doi: 10.1101/2024.09.14.609619> for more details.

Install

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

install.packages("easybio", 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("person-c/easybio")

Development version from person-c/easybio. 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-easybio

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-easybio

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-easybio

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

Health

CRAN checks

13OK

Slowest check: 3.1 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.02

1.8%

Coverage · measured lines

100%

Documentation · exports

6

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
OK2026-04-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-04-09
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 74 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 71%
Documented parameters: 99%
Return-value docs: 100%
References docs: 0%

Downloads

4.1K

CRAN downloads in the past year

Rank #10,014 · ~11/day · ~340/mo

Releases R versions

Daily download trend is not available in this view yet.

31630 days

94590 days

4.1K1 year

Compare downloads with other packages →

Also on195 r2u20 autocran

Repository

GitHub ↗ person-c/easybio

15Stars

1Forks

0Open issues

1Open PRs

1Releases

129Commits

1Contributors

bioinformaticsrna-seqgseasingle-cellcellmarker2

129 commits · Last activity 2026-07-21 · +7.1% stars, 30d

Stars over time

2025-03-31 · 112026-08-18 · 15

Repository practices

Upstream repositoryBeta

7 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/person-c/easybio on 2026-08-16.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (2)

lintrRStudio project

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (6)

data.table checkmate ggplot2 httr2 R6 xml2

LinkingTo (0)

none

Suggests (9)

litedown patchwork ggrepel Seurat limma GEOquery fgsea edgeR testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Wei Cui

Author, Maintainer, Copyright holder

Authors (1)

Wei Cui

Author, Maintainer, Copyright holder

Copyright holders (1)

Wei Cui

Author, Maintainer, Copyright holder

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.2.3Latest
2025-10-02 · current release · diff ↗
1.2.2
2025-09-01 · diff ↗
1.2.1
2025-08-30 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.1.1
2025-02-12 · diff ↗
1.1.0
2024-09-16 · diff ↗
1.0.1
2024-09-08 · diff ↗
1.0
2024-09-05
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-09-05
Total releases: 7 / 2 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 1.6 MB / 2 files
Download size: 3.2 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("easybio")

Format

Cui, W. (2025). easybio: Comprehensive Single-Cell Annotation and Transcriptomic Analysis Toolkit (Version 1.2.3) [Computer software]. https://doi.org/10.32614/CRAN.package.easybio

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 easybio version 1.2.3 [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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