R Observatory: Metrics for ZetaSuite version 1.0.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ZetaSuite

1.0.3Package record

Analyze High-Dimensional High-Throughput Dataset and Quality Control Single-Cell RNA-Seq

0packages depend

3.8Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Junhui LiCRAN page ↗GitHub ↗Issues ↗Declared funder: Xiang-Dong Fu

The advent of genomic technologies has enabled the generation of two-dimensional or even multi-dimensional high-throughput data, e.g., monitoring multiple changes in gene expression in genome-wide siRNA screens across many different cell types (E Robert McDonald 3rd (2017) <doi: 10.1016/j.cell.2017.07.005> and Tsherniak A (2017) <doi: 10.1016/j.cell.2017.06.010>) or single cell transcriptomics under different experimental conditions. We found that simple computational methods based on a single statistical criterion is no longer adequate for analyzing such multi-dimensional data. We herein introduce 'ZetaSuite', a statistical package initially designed to score hits from two-dimensional RNAi screens.We also illustrate a unique utility of 'ZetaSuite' in analyzing single cell transcriptomics to differentiate rare cells from damaged ones (Vento-Tormo R (2018) <doi: 10.1038/s41586-018-0698-6>). In 'ZetaSuite', we have the following steps: QC of input datasets, normalization using Z-transformation, Zeta score calculation and hits selection based on defined Screen Strength.

Install

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

install.packages("ZetaSuite", 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("JunhuiLi1017/ZetaSuite")

Development version from JunhuiLi1017/ZetaSuite. 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-zetasuite

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-ZetaSuite

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-ZetaSuite

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: 5.1 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.3

READMEYes · 226 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 15
Examples that run: 93%14 run in a plain check · 1 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 7%

Vignettes (1)

ZetaSuite HTML

How these are measured

Downloads

3.8K

CRAN downloads in the past year

Rank #10,673 · ~10/day · ~314/mo

Releases R versions

Daily download trend is not available in this view yet.

33430 days

98190 days

3.8K1 year

Compare downloads with other packages →

Also on131 r2u2 autocran

How downloads are counted

Repository

junhuili1017/zetasuite ↗Account: JunhuiLi1017

0Stars

0Forks

0Open issues

0Open PRs

0Releases

Last activity 2025-09-24 · The default branch showed an older version (1.0.2) than CRAN on 2026-10-21

Responsiveness

not measured

How these are measured

PracticesBeta

Checks run against github.com/junhuili1017/zetasuite on 2026-10-21.

No development-tooling practices detected in the upstream repository.

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Installing ZetaSuite adds 81 packages (45 with compiled code, 74 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 2.10

Imports (12)

RColorBrewer Rtsne e1071 ggplot2 reshape2 gridExtra mixtools shinyjs shinydashboard shiny plotly DT

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

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 (5)

Junhui Li

Author, Maintainer since 1.0.0 (2022)

Author

Contributor

Contributor

Copyright holder, Funder

Releases (4)

Pick two releases to compare their code metrics.

1.0.3Latest
record
2026-04-28 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.0.2
record
2025-09-24 · diff ↗ ·
added 1 export
ZetaSuiteApp
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.0.1
record
2022-05-24 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0.0
record
2022-03-31
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2022-03-31
Total releases: 4 / 4 yrs
License: MIT + file LICENSE OSI · relicensed from GPL-2 | GPL-3 in 1.0.2
Minimum R: ≥ 2.10
Bundled data: 3.5 MB / 8 files
Download size: 4.2 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ZetaSuite")

Format

Li, J., Fu, X., Hao, Y., Zhang, S., & Zhao, G. (2026). ZetaSuite: Analyze High-Dimensional High-Throughput Dataset and Quality Control Single-Cell RNA-Seq (Version 1.0.3) [Computer software]. https://doi.org/10.32614/CRAN.package.ZetaSuite

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 ZetaSuite version 1.0.3 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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