R Observatory: Metrics for coFAST version 0.3.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

coFAST

0.3.0Package record

Spatially-Aware Cell Clustering Algorithm with Cluster Significant Assessment

0packages depend

2.8Kdownloads / year

–test coverage

12/13flavors OK

Overview

About

Maintained by Wei LiuCRAN page ↗GitHub ↗Issues ↗

A spatially-aware cell clustering algorithm is provided with cluster significance assessment. It comprises four key modules: spatially-aware cell-gene co-embedding, cell clustering, signature gene identification, and cluster significant assessment. More details can be referred to Peng Xie, et al. (2025) doi:10.1016/j.cell.2025.05.035.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("coFAST", 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("feiyoung/coFAST")

Development version from feiyoung/coFAST. 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-cofast

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

Health

CRAN checks

1ERROR12OK

Check messages

ERRORwhether package can be installedr-oldrel-macos-arm64

Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.5/coFAST.Rcheck/00install.out’ for details.

CRAN check page ↗

Slowest check: 7.6 min · r-oldrel-windows-x86_64

Status changes

ERROR12 OK, 1 ERRORNow
ERROR11 OK, 3 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.3.0

READMEYes · 622 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileNo

Help pages: 15
Examples that run: 100%15 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 60%

Vignettes (1)

coFAST: NSCLC CosMx data coembedding HTML

How these are measured

Downloads

2.8K

CRAN downloads in the past year

Rank #10,131 · ~8/day · ~237/mo

Releases R versions

Daily download trend is not available in this view yet.

38130 days

98390 days

2.8K1 year

Compare downloads with other packages →

Also on429 r2u

How downloads are counted

Repository

feiyoung/cofast ↗Account: feiyoung

1Stars

0Forks

0Open issues

0Open PRs

0Releases

8Commits

1Commit identities

8 commits · Last activity 2026-06-05 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 59
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2026-07-07 · 02026-08-25 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/feiyoung/cofast on 2026-10-11.

Docs source (1)

GitHub Pages site last deployed 2026-06-05

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

21 external dependencies (excludes base and recommended)

Installing coFAST adds 146 packages (86 with compiled code, 138 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB. 1 more not on CRAN is not measured.

Depends (1)

R >= 4.0.0

Imports (16)

Rcpp furrr purrr future ggplot2 irlba DR.SC ProFASTMatrixade4 progress pbapply dplyr Seuratstatsutils

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (7)

knitr rmarkdown scater PRECAST ggrepel RANNgrDevices

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 (6)

Wei Liu

Author, Maintainer since 0.1.0 (2025)

Author

Author

Author

Author

Author

Releases (3)

Pick two releases to compare their code metrics.

0.3.0Latest
record
2026-06-04 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
0.2.0
record
2025-12-14 · diff ↗
0.1.0
record
2025-11-17
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-11-17
Total releases: 3 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.0.0
Bundled data: 2.0 MB / 3 files
Download size: 2.0 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("coFAST")

Format

Liu, W., Lin, C., Liu, J., Xie, P., Yang, Y., & Zhang, X. (2026). coFAST: Spatially-Aware Cell Clustering Algorithm with Cluster Significant Assessment (Version 0.3.0) [Computer software]. https://doi.org/10.32614/CRAN.package.coFAST

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 coFAST version 0.3.0 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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