R Observatory: Metrics for SoupX version 1.6.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SoupX

1.6.2

Single Cell mRNA Soup eXterminator

1packages depend

29.1Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Matthew Daniel YoungFirst published 2020-05-266 releasesCRAN page ↗GitHub ↗

Quantify, profile and remove ambient mRNA contamination (the "soup") from droplet based single cell RNA-seq experiments. Implements the method described in Young et al. (2018) doi:10.1101/303727.

Install

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

install.packages("SoupX", 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("constantAmateur/SoupX")

Development version from constantAmateur/SoupX. 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-soupx

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-SoupX

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-SoupX

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

Health

CRAN checks

2NOTE11OK

Failing flavors

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

Slowest check: 8.0 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

4

Dependencies · direct

Check history

NOTE2026-06-09
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
11 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-10
9 OK · 5 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
9 OK · 4 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
9 OK · 5 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,493 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

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

Downloads

29.1K

CRAN downloads in the past year

Rank #2,631 · ~80/day · ~2.4K/mo

Releases R versions

Daily download trend is not available in this view yet.

2.3K30 days

6.6K90 days

29.1K1 year

Compare downloads with other packages →

Also on1.4K r2u4 autocran7.2K conda_forge20 c2d4u

Repository

GitHub ↗ constantamateur/soupx

338Stars

43Forks

50Open issues

0Open PRs

0Releases

111Commits

6Contributors

111 commits · Last activity 2022-11-01 · +0.9% stars, 30d

Stars over time

2026-07-14 · 3342026-08-24 · 338

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/constantamateur/soupx on 2026-08-23.

CRAN release process (1)

cran-comments.md

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

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (4)

ggplot2MatrixmethodsSeurat

LinkingTo (0)

none

Suggests (5)

knitr rstan DropletUtils rmarkdown formatR

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

CRMetrics

Code & Tests

Datasets

People & History

People (0)

Author records are not tracked yet for this package.

Listed in earlier versions (1)

Matthew Daniel Young

no longer listed · 1.4.5 to 1.6.2

Package Timeline

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

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
R
R 4.3.0 released · 2023-04-21
1.6.2Latest
2022-11-01 · current release · diff ↗
1.6.1
2022-05-26 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.5.2
2021-05-17 · diff ↗
unarchivedReturned to CRAN
2021-05-17
archivedRemoved from CRAN
2021-04-10
check problems were not corrected in time
1.5.0
2021-01-13 · diff ↗
1.4.8
2020-10-15 · diff ↗
1.4.5
2020-05-26
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-05-26
Total releases: 6 / 6 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.5.0
Bundled data: 3.8 MB / 4 files
Download size: 4.7 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SoupX")

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 SoupX version 1.6.2 [Data set]. HJJB, LLC. Data release v2026-08-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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