ZetaSuite

1.0.3

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

0packages depend

3.6Kdownloads / year

–test coverage

12/13checks pass

Overview

About

Maintained by Junhui LiFirst published 2022-03-314 releasesCRAN page ↗GitHub ↗

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.

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).

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 5.9 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

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
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 226 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 93%
Documented parameters: 100%
Return-value docs: 100%
References docs: 7%

Downloads

3.6K

CRAN downloads in the past year

Rank #7,142 · ~10/day · ~301/mo

Releases R versions

Daily download trend is not available in this view yet.

33830 days

1.3K90 days

3.6K1 year

Compare downloads with other packages →

Also on183 r2u2 autocran

Repository

GitHub ↗ junhuili1017/zetasuite

0Stars

0Forks

0Open issues

0Open PRs

0Releases

Last activity 2025-09-24

Repository practices

Upstream repositoryBeta

Checks run against github.com/junhuili1017/zetasuite on 2026-07-30.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

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.

Code & Tests

Datasets

People & History

People (5)

Maintainer (1)

Junhui Li

Author, Maintainer

Authors (2)

Junhui Li

Author, Maintainer

Yajing Hao

Author

Contributors (2)

Contributor

Contributor

Funders (1)

Package Timeline

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

1.0.3Latest
2026-04-28 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.0.2
2025-09-24 · diff ↗
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
2022-05-24 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0.0
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
Minimum R: ≥ 2.10
Bundled data: 3.5 MB / 8 files
Download size: 4.2 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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