R Observatory: Metrics for scCustomize version 3.3.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

scCustomize

3.3.0Package record

Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

0packages depend

45Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Samuel MarshCRAN page ↗GitHub ↗Website ↗Issues ↗

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.

Changes in 3.3.0

Added

Added reorder, reorder_decreasing, and plot_median parameters to Plot_Cells_per_Sample when grouping by sample.
Added Read_Velocity function to enable reading of velocyto loom output files without needing to install velocyto.R package (which currently suffers from significant installation issues unrelated to reading loom files).
Added ability to pass plot_type in ElbowPlot_scCustom for users with Seurat version 5.5.0+.
Added ability to create "variance" or "cumulative variance" plot types in ElbowPlot_scCustom for users with Seurat version below 5.5.0.

Changed

**BREAKING CHANGE** The plot_by parameter has been soft-deprecated in Seq_QC_Plot_* family of functions. Please use group.by instead. Using plot_by will warn user but still work until scCustomize v3.5.0.
**BREAKING CHANGE** The parameter cutoff_line_width has been soft-deprecated in QC_Plot_* family of functions. Please use cutoff_linewidth instead. Using cutoff_line_width will warn user but still work until scCustomize v3.5.0.
**BREAKING CHANGE** The parameter linewidth has been soft-deprecated in ElbowPlot_scCustom function. Please use cutoff_linewidth instead. Using linewidth will warn user but still work until scCustomize v3.5.0.
Add some checks for appropriate ... usage.

Fixes

Fixed default setting of linewidth parameter in geom_hline and geom_vline calls to avoid unnecessary empty aesthetic warnings in ggplot2 4.0.0+.

Show all changes in 3.3.0Hide the rest of the changes in 3.3.0

Fixed warning in Dataset_Size_LIGER due to deprecation in Extract_Sample_Meta.
Fixed issue with group colors in in DimPlot_scCustom when split only contains one group Thanks @zrlewis, (#262).
All vignettes updated to use qs2 package as qs package is now fully deprecated.

From NEWS.md in the release

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. 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-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). 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: 9.2 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-10-15
ERROR12 OK, 1 ERROR2026-09-25
OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK, 1 FAILURE2026-06-08

Show 7 earlier changesHide 7 earlier changes

ERROR12 OK, 1 ERROR2026-06-07
OK12 OK2026-04-25
NOTE13 OK, 1 NOTE2026-04-10
ERROR12 OK, 1 NOTE, 1 ERROR2026-04-09
NOTE13 OK, 1 NOTE2026-03-27
WARNING12 OK, 1 NOTE, 1 WARNING2026-03-26
NOTE13 OK, 1 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 3.3.0

READMEYes · 254 wordsVignettes· In the repository, left out of the releaseNEWSYes · 100% structured · mentions 3.3.0Citation fileNoWebsiteYes · pkgdown

The repository also keeps web-only articles.

Help pages: 174 (2 internal)includes a package overview page
Examples that run: 25%40 run in a plain check · 3 only when donttest examples are enabled (R CMD check --as-cran) · 116 never run · 1 hold no code
Exported functions with examples: 99%
Documented parameters: 100%
Return-value docs: 97%
Help pages citing references: 18%

How these are measured

Downloads

45K

CRAN downloads in the past year

Rank #2,243 · ~123/day · ~3.8K/mo

Releases R versions

Daily download trend is not available in this view yet.

2.3K30 days

7.6K90 days

45K1 year

Compare downloads with other packages →

Also on650 r2u4 autocran8.7K conda_forge

How downloads are counted

Repository

samuel-marsh/sccustomize ↗Account: samuel-marsh

314Stars

33Forks

10Open issues

0Open PRs

23Releases

3,873Commits

5Commit identities

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

License file reads as GPL-3.0 · 3,873 commits · Last activity 2026-05-11 · +1% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 76%
Median days to close, 50 most recently updated closed issues: 6
Median days to close, 50 most recently updated closed PRs: 2

Stars over time

2025-10-09 · 2742026-10-15 · 314

How these are measured

PracticesBeta

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

Checks run against github.com/samuel-marsh/sccustomize on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (1)

Issue templates

Docs source (2)

pkgdown

GitHub Pages site last deployed 2026-05-11

pkgdown site last built 2026-05-11

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 2 practices

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

46 external dependencies (excludes base and recommended)

Installing scCustomize adds 159 packages (89 with compiled code, 151 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (5)

Samuel Marsh

Author, Maintainer since 1.1.0 (2022)

Zoe Clarke

Contributor · added in 3.1.3

Lucas Graybuck

Contributor

Velina Kozareva

Contributor

Ming Tang

Contributor

Releases (18)

Pick two releases to compare their code metrics.

3.3.0Latest
record
2026-05-08 · current release · diff ↗ ·
added 1 export
Read_Velocity
R
R 4.6.0 released · 2026-04-24
3.2.4
record
2025-12-11 · diff ↗
3.2.3
record
2025-12-09 · diff ↗
3.2.2
record
2025-11-13 · diff ↗
3.2.1
record
2025-11-08 · diff ↗ ·
removed 2 exports
Add_Top_Gene_Pct_Seurat, Liger_to_Seurat

added 2 exports
ElbowPlot_scCustom, Map_New_Meta
3.2.0
record
2025-09-10 · diff ↗ ·
added 1 export
ReFilter_SeuratObject
3.1.3
record
2025-08-26 · diff ↗ ·
removed 7 exports
Add_Cell_Complexity_LIGER, Add_Cell_Complexity_Seurat, Add_Mito_Ribo_LIGER, Add_Mito_Ribo_Seurat, Gene_Present, Meta_Present_LIGER, Split_FeatureScatter

added 6 exports
Add_MALAT1_Threshold, Dataset_Size_LIGER, Get_Reference_LIGER, Proportion_Plot_per_Sample, Read_Add_cNMF, exAM_Scoring
R
R 4.5.0 released · 2025-04-11
3.0.1
record
2024-12-18 · diff ↗
3.0.0
record
2024-12-05 · diff ↗ ·
removed 1 export
LIGER_Features

added 19 exports
Idents<-, Add_Hemo, Add_Top_Gene_Pct, Cells, Cells_by_Identities_LIGER, Cells_per_Sample, Embeddings, Factor_Cor_Plot, Features, Find_Factor_Cor, Idents, Proportion_Plot, Random_Cells_Downsample, Read_Metrics_CellBender, SpatialDimPlot_scCustom, Subset_LIGER, Updated_MGI_Symbols, WhichCells, seq_zeros
R
R 4.4.0 released · 2024-04-24
2.1.2
record
2024-02-28 · diff ↗
2.1.1
record
2024-02-24 · diff ↗
2.1.0
record
2024-02-23 · diff ↗ ·
added 12 exports
Add_Alt_Feature_ID, Add_Cell_Complexity, Add_Mito_Ribo, Convert_Assay, Feature_Present, LIGER_Features, Split_Layers, Split_Vector, Updated_HGNC_Symbols, as.LIGER, as.Seurat, as.anndata
2.0.1
record
2023-11-17 · diff ↗

Show 7 earlier eventsHide 7 earlier events

2.0.0
record
2023-11-14 · diff ↗ ·
added 7 exports
Add_Cell_QC_Metrics, Add_Top_Gene_Pct_Seurat, Barcode_Plot, FeatureScatter_scCustom, Iterate_Barcode_Rank_Plot, MAD_Stats, QC_Histogram
1.1.3
record
2023-07-19 · diff ↗
1.1.2
record
2023-07-18 · diff ↗ ·
added 3 exports
Extract_Modality, Merge_Sparse_Multimodal_All, Reduction_Loading_Present
R
R 4.3.0 released · 2023-04-21
1.1.1
record
2023-01-13 · diff ↗
1.1.0
record
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

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("scCustomize")

Format

Marsh, S., Clarke, Z., Graybuck, L., Kozareva, V., & Tang, M. (2026). scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing (Version 3.3.0) [Computer software]. https://doi.org/10.32614/CRAN.package.scCustomize

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 scCustomize version 3.3.0 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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