R Observatory: Metrics for Cleanet version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Cleanet

1.0.0Package record

Automated Doublet Detection and Classification for Cytometry Data

0packages depend

2.5Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Matei IonitaCRAN page ↗

Automated method for doublet detection in flow or mass cytometry data, based on simulating doublets and finding events whose protein expression patterns are similar to the simulated doublets.

Install

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

install.packages("Cleanet", 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-cleanet

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-Cleanet

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-Cleanet

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: 3.9 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-04-22
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18

Show 1 earlier changeHide 1 earlier change

NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.0

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 5
Examples that run: 100%4 run in a plain check
Exported functions with examples: 80%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Cleanet for Mass Cytometry HTML

How these are measured

Downloads

2.5K

CRAN downloads in the past year

Rank #18,387 · ~7/day · ~207/mo

Releases R versions

Daily download trend is not available in this view yet.

20830 days

71590 days

2.5K1 year

Compare downloads with other packages →

Also on363 r2u6 autocran

How downloads are counted

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Installing Cleanet adds 44 packages (25 with compiled code, 34 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, Rcpp 1.8 MB.

Depends (1)

R >= 3.5

Imports (10)

Rcpp RcppHNSW ggplot2 dplyr tidyr readr reshape2 tibble magrittrmethods

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (3)

knitr rmarkdown vctrs

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 (1)

Matei Ionita

Author, Maintainer since 1.0.0 (2024)

Releases (1)

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.0.0Latest
record
2024-12-19 · current release
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-12-19
Total releases: 1 / 2 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5
Download size: 2.5 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("Cleanet")

Format

Ionita, M. (2024). Cleanet: Automated Doublet Detection and Classification for Cytometry Data (Version 1.0.0) [Computer software]. https://doi.org/10.32614/CRAN.package.Cleanet

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 Cleanet version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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