R Observatory: Metrics for scCATCH version 3.2.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

scCATCH

3.2.2Package record

Single Cell Cluster-Based Annotation Toolkit for Cellular Heterogeneity

0packages depend

6.2Kdownloads / year

2.2%test coverage

11/13flavors OK

Overview

About

Maintained by Xin ShaoCRAN page ↗GitHub ↗

An automatic cluster-based annotation pipeline based on evidence-based score by matching the marker genes with known cell markers in tissue-specific cell taxonomy reference database for single-cell RNA-seq data. See Shao X, et al (2020) doi:10.1016/j.isci.2020.100882 for more details.

Install

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

install.packages("scCATCH", 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("ZJUFanLab/scCATCH")

Development version from ZJUFanLab/scCATCH. 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-sccatch

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-scCATCH

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-scCATCH

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

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Xin Shao<xin_shao@zju.edu.cn>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Xin",
                    family = "Shao",
                    role = c("aut", "cre"),
                    email = "xin_shao@zju.edu.cn")
as necessary.

CRAN check page ↗

Slowest check: 4.9 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 3.2.2

READMEYes · 336 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 10
Examples that run: 100%3 run in a plain check
Exported functions with examples: 43%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

scCATCH tutorial

How these are measured

Downloads

6.2K

CRAN downloads in the past year

Rank #5,905 · ~17/day · ~514/mo

Releases R versions

Daily download trend is not available in this view yet.

44130 days

1.4K90 days

6.2K1 year

Compare downloads with other packages →

Also on188 r2u20 autocran

How downloads are counted

Repository

zjufanlab/sccatch ↗Account: ZJUFanLab

247Stars

35Forks

5Open issues

0Open PRs

4Releases

118Commits

5Commit identities

marker-genescell-markerscluster-annotationseuratsingle-cellrna-seqtranscriptomicssequencing

License file reads as GPL-3.0 · 118 commits · Last activity 2023-05-08 · +0.4% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 8
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-10-11 · 2312026-09-24 · 247

How these are measured

PracticesBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/zjufanlab/sccatch on 2026-10-11.

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing scCATCH adds 17 packages (9 with compiled code, 17 MB of source tarballs). Heaviest: stringi 11 MB, Rcpp 1.8 MB, vctrs 1.0 MB.

Depends (1)

R >= 4.0.0

Imports (5)

Matrixmethodsprogressstatsreshape2

LinkingTo (0)

none

Suggests (4)

rmarkdown knitr testthat prettydoc

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 (from the free-text Author field) (1)

Xin Shao

Maintainer since 3.0 (2022)

Releases (5)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
3.2.2Latest
record
2023-04-23 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
3.2.1
record
2022-11-07 · diff ↗
3.2
record
2022-09-14 · diff ↗
3.1
record
2022-05-14 · diff ↗
R
R 4.2.0 released · 2022-04-22
3.0
record
2022-01-07
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2022-01-07
Total releases: 5 / 4 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.0.0
Bundled data: 1.1 MB / 2 files
Download size: 1.8 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("scCATCH")

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

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 scCATCH version 3.2.2 [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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