scCustomize

3.3.0

Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

0packages depend

52.2Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Samuel MarshFirst published 2022-12-2318 releasesCRAN page ↗GitHub ↗

Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'. 'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions. For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing" doi:10.5281/zenodo.5706430 RRID:SCR_024675.

Install

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

install.packages("scCustomize", 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("samuel-marsh/scCustomize")

Development version from samuel-marsh/scCustomize. 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-sccustomize

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-scCustomize

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-scCustomize

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

Health

CRAN checks

13OK

Slowest check: 10.5 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

OK2026-06-08
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 1 FAILURE
ERROR2026-06-07
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-10
13 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
12 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 3 earlier snapshots

NOTE2026-03-27
13 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-03-26
12 OK · 1 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
13 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 254 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 31%
Documented parameters: 100%
Return-value docs: 97%
References docs: 18%

Downloads

52.2K

CRAN downloads in the past year

Rank #2,051 · ~143/day · ~4.4K/mo

Releases R versions

Daily download trend is not available in this view yet.

3.6K30 days

11.9K90 days

52.2K1 year

Compare downloads with other packages →

Also on239 r2u9 autocran4.1K conda_forge

Repository

GitHub ↗ samuel-marsh/sccustomize

304Stars

35Forks

8Open issues

0Open PRs

23Releases

3,873Commits

5Contributors

customizationggplot2seuratsingle-cellsingle-cell-genomicssingle-cell-rna-seqvisualizationscrna-seq

License GPL-3.0 · 3,873 commits · Last activity 2026-06-30 · +0.7% stars, 30d

Stars over time

2025-07-18 · 2632026-07-18 · 304

Repository practices

Upstream repositoryBeta

6 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/samuel-marsh/sccustomize on 2026-07-19.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

Show all practices

Governance and community (1)

Issue templates

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

Dependencies

Declared dependencies

46 external dependencies (excludes base and recommended)

Depends (2)

R >= 4.0.0Seurat

Imports (33)

circlize cli cowplot data.table dplyr forcats ggbeeswarm ggplot2 ggprism ggrastr ggrepel gluegrDevicesgridjanitor lifecycle magrittr Matrix (>= 1.5.0)mcprogressmethodspaletteer patchwork pbapply purrr rlang scales scattermore SeuratObjectstatsstringi stringr tibble tidyr

LinkingTo (0)

none

Suggests (16)

BiocFileCache ComplexHeatmap dittoSeq DropletUtils ggpubr hdf5r knitr Nebulosa remotes reticulate rliger rmarkdown scuttle tidyselect qs2 viridis

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 32,256 (77%)Rd 9,773 (23%)

Code characteristics

Object systems

S328

Cyclomatic complexity: 7.0 median / 62 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

276 153 exported

Complexity

10 avg / 62 max

Call network

276 nodes / 538 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (5)

Maintainer (1)

Samuel Marsh

Author, Maintainer

Authors (1)

Samuel Marsh

Author, Maintainer

Contributors (4)

Zoe Clarke

Contributor · added in 3.1.3

Lucas Graybuck

Contributor

Velina Kozareva

Contributor

Ming Tang

Contributor

Package Timeline

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

3.3.0Latest
2026-05-08 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
3.2.4
2025-12-11 · diff ↗
3.2.3
2025-12-09 · diff ↗
3.2.2
2025-11-13 · diff ↗
3.2.1
2025-11-08 · diff ↗
3.2.0
2025-09-10 · diff ↗
3.1.3
2025-08-26 · diff ↗
R
R 4.5.0 released · 2025-04-11
3.0.1
2024-12-18 · diff ↗
3.0.0
2024-12-05 · diff ↗
R
R 4.4.0 released · 2024-04-24
2.1.2
2024-02-28 · diff ↗
2.1.1
2024-02-24 · diff ↗
2.1.0
2024-02-23 · diff ↗
2.0.1
2023-11-17 · diff ↗

Show 7 earlier events

2.0.0
2023-11-14 · diff ↗
1.1.3
2023-07-19 · diff ↗
1.1.2
2023-07-18 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.1.1
2023-01-13 · diff ↗
1.1.0
2022-12-23
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-12-23
Total releases: 18 / 4 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.0.0
Bundled data: 303 KB / 12 files
Download size: 1.5 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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