R Observatory: Metrics for scRNAstat version 0.1.1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

scRNAstat

0.1.1.2

A Pipeline to Process Single Cell RNAseq Data

0packages depend

8.9Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Yonghe XiaFirst published 2021-09-223 releasesCRAN page ↗

A pipeline that can process single or multiple Single Cell RNAseq samples primarily specializes in Clustering and Dimensionality Reduction. Meanwhile we use common cell type marker genes for T cells, B cells, Myeloid cells, Epithelial cells, and stromal cells (Fiboblast, Endothelial cells, Pericyte, Smooth muscle cells) to visualize the Seurat clusters, to facilitate labeling them by biological names. Once users named each cluster, they can evaluate the quality of them again and find the de novo marker genes also.

Install

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

install.packages("scRNAstat", 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-scrnastat

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-scRNAstat

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-scRNAstat

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

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc

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

Code health

None

Tests · ratio 0.00

not tracked

Coverage

83%

Documentation · exports

10

Dependencies · direct

Check history

NOTE2026-06-09
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
10 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-05-20
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-04-23
11 OK · 0 NOTE · 3 WARNING · 0 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

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 40%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

8.9K

CRAN downloads in the past year

Rank #4,500 · ~24/day · ~740/mo

Releases R versions

Daily download trend is not available in this view yet.

43430 days

1.8K90 days

8.9K1 year

Compare downloads with other packages →

Also on178 r2u7 autocran

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (10)

Seurat ggplot2 stringr clustree magrittrMatrixdplyr patchwork colorspace DBI

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Yonghe Xia

Contributor, Maintainer

Authors (1)

Jianming Zeng

Author

Contributors (1)

Yonghe Xia

Contributor, Maintainer

Copyright holders (1)

Biotrainee group

Copyright holder, Funder

Funders (1)

Biotrainee group

Copyright holder, Funder

Package Timeline

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

0.1.1.2Latest
2026-05-15 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.1.1.1
2025-03-08 · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.1.1
2021-09-22
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-09-22
Total releases: 3 / 5 yrs
License: AGPL (>= 3) OSI
Minimum R: ≥ 2.10
Bundled data: 2.3 MB / 2 files
Download size: 2.3 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("scRNAstat")

Format

Xia, Y., Biotrainee group, & Zeng, J. (2026). scRNAstat: A Pipeline to Process Single Cell RNAseq Data (Version 0.1.1.2) [Computer software]. https://doi.org/10.32614/CRAN.package.scRNAstat

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 scRNAstat version 0.1.1.2 [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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