Journal Article

DKFZ-2026-01513

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png SCpubr: a user-friendly R-package for generating publication-ready visualizations of single-cell transcriptome analyses.

Blanco-Carmona, E.DKFZ* ; Kool, M. (Last author)DKFZ*

2026
Oxford University Press Oxford

Abstract: Single-cell RNA sequencing (scRNA-seq) is now a core technology for resolving cellular heterogeneity in complex samples, and standard analysis workflows produce a wide range of outputs, each requiring tailored visualization. To support this, a wide range of analysis tools have been developed, many of which offer built-in visualizations but leave further customization to the user. Researchers who run standard single-cell workflows in R, often experimental biologists with a working knowledge of Seurat and ggplot2, still spend considerable effort converting analytical outputs into figures that meet journal standards.We present SCpubr, an R package that provides concise function calls for generating high-quality, publication-ready visualizations commonly used in single-cell transcriptome analyses.SCpubr is available on CRAN (https://cran.r-project.org/package=SCpubr), with source code accessible on GitHub (https://github.com/enblacar/SCpubr).Supplementary figures are available at Bioinformatics Advances online. Extensive documentation and tutorials are available via the GitHub Pages site (https://enblacar.github.io/SCpubr-book/). The complete analysis code used to generate all figures in this publication, along with the full R session information and instructions for obtaining the raw input data, is available in GitHub (https://github.com/enblacar/SCpubr-manuscript).

Note: #LA:B062#

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Contributing Institute(s):

1. DKTK HD zentral (HD01)
2. Pädiatrische Neuroonkologie (B062)

Research Program(s):

1. 312 - Funktionelle und strukturelle Genomforschung (POF4-312) (POF4-312)

Appears in the scientific report 2026

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Database coverage:
; ; ; Article Processing Charges ; BIOSIS Previews ; Biological Abstracts ; Clarivate Analytics Master Journal List ; DOAJ Seal ; Emerging Sources Citation Index ; Fees ; PubMed Central ; SCOPUS ; Web of Science Core Collection

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