R Observatory: Metrics for SoupX version 1.6.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SoupX

1.6.2Package record

Single Cell mRNA Soup eXterminator

0packages dependsuggested by 1

28.9Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Matthew Daniel YoungCRAN 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. 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-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). 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

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Matthew Daniel Young <my4@sanger.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Matthew", "Daniel"),
                    family = "Young",
                    role = c("aut", "cre"),
                    email = "my4@sanger.ac.uk")
as necessary.

CRAN check page ↗

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

Status changes

NOTE11 OK, 2 NOTE2026-09-08
ERROR10 OK, 2 NOTE, 1 ERROR2026-09-07
NOTE11 OK, 2 NOTE2026-06-09
ERROR11 OK, 1 NOTE, 1 ERROR2026-06-08
NOTE9 OK, 5 NOTE2026-04-10

Show 2 earlier changesHide 2 earlier changes

ERROR9 OK, 4 NOTE, 1 ERROR2026-04-09
NOTE9 OK, 5 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.6.2

READMEYes · 1,493 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 24includes a package overview page
Examples that run: 100%15 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

PBMC Demonstration

How these are measured

Downloads

28.9K

CRAN downloads in the past year

Rank #1,810 · ~79/day · ~2.4K/mo

Releases R versions

Daily download trend is not available in this view yet.

5.6K30 days

11.1K90 days

28.9K1 year

Compare downloads with other packages →

Also on2.5K r2u6 autocran8K conda_forge75 c2d4u

How downloads are counted

Repository

constantamateur/soupx ↗Account: constantAmateur

346Stars

45Forks

50Open issues

0Open PRs

0Releases

111Commits

6Commit identities

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

Responsiveness

How these are sampled

PRs merged (all time): 88%
Median days to close, 50 most recently updated closed issues: 57
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2026-07-14 · 3342026-10-15 · 346

How these are measured

PracticesBeta

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

Checks run against github.com/constantamateur/soupx on 2026-10-11.

CRAN release process (1)

cran-comments.md

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing SoupX adds 135 packages (81 with compiled code, 127 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB.

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

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

CRMetrics

How these are counted

Code & Tests

Datasets

People & History

People (from the free-text Author field) (1)

Matthew Daniel Young

Maintainer since 1.4.5 (2020)

Releases (6)

Pick two releases to compare their code metrics.

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

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")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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