ArticleBioinformatics advances2026
SCpubr: a user-friendly R-package for generating publication-ready visualizations of single-cell transcriptome analyses.
Article in Bioinformatics advances, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers, 1 of them a synthesis that pooled it.
What it found
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Who cites it
35 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Therapeutic bacteria-trained NK cells confer long-term protection against cancer metastasis.Molecular therapy : the journal of the American Society of Gene Therapy · 2026Article
- Immunogenetic and Transcriptomic Evidence Implicating the NKG2D-MICA/MICB Axis in CALR-Mutated Myeloproliferative Neoplasms.Cancers · 2026Article
- Volitional cocaine taking engages distinct medium spiny neuron and astrocyte transcriptional programs in the rat nucleus accumbens.bioRxiv : the preprint server for biology · 2026Article
- STAT4 drives optimal expansion and transcriptional repression of type I interferon pathway in inflammatory ILC2.Cellular and molecular life sciences : CMLS · 2026Article
- IGSF11-VISTA is a critical and targetable immune checkpoint axis in diffuse midline glioma.Cancer cell · 2026Article
- An integrative omics-guided druggability analysis of VCX2 in hepatocellular carcinoma using Peruvian natural products.Frontiers in bioinformatics · 2026Article
- Reversing T cell dysfunction in a novelFrontiers in immunology · 2026Article
- Deep profiling of human T cells defines compartmentalized clones and phenotypic trajectories across blood and tonsils.Immunity · 2025Article
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- Exploring cellular changes in ruptured human quadriceps tendons at single-cell resolution.The Journal of physiology · 2025Article
- GPX1 and RCN1 as New Endoplasmic Reticulum Stress-Related Biomarkers in Multiple Sclerosis Brain Tissue and Their Involvement in the APP-CD74 Pathway: An Integrated Study Combining Machine Learning and Multi-Omics.International journal of molecular sciences · 2025Article
- Regulatory T cell therapy is associated with distinct immune regulatory lymphocytic infiltrates in kidney transplants.Med (New York, N.Y.) · 2025Article
- Heterogeneous and novel transcript expression in single cells of patient-derived clear cell renal cell carcinoma organoids.Genome research · 2025Article
- Integration of Transcriptomic and Single-Cell Data to Uncover Senescence- and Ferroptosis-Associated Biomarkers in Sepsis.Biomedicines · 2025Article
- Convergent state-control of endogenous opioid analgesia.bioRxiv : the preprint server for biology · 2025Article
- Unraveling the phenotypic states of human innate-like T cells: Comparative insights with conventional T cells and mouse models.Cell reports · 2024Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Motivation: 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. Results: 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. Availability and implementation: SCpubr is available on CRAN (https://cran.r-project.org/package=SCpubr), with source code accessible on GitHub (https://github.com/enblacar/SCpubr). Supplementary information: 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).
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.