Stachelek Kevin, Bhat Bhavana, Cobrinik David
The Vision Center, Department of Surgery, and Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA.
Cancer Biology and Genomics Program, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
GigaByte. 2025 Jun 24;2025:gigabyte158. doi: 10.46471/gigabyte.158. eCollection 2025.
Chevreul is an open-source R Bioconductor package and interactive R Shiny app for processing and visualising single-cell RNA sequencing (scRNA-seq) data. Chevreul differs from other scRNA-seq analysis packages in its ease of use, capacity to analyze full-length RNA sequencing data for exon coverage and transcript isoform inference, and support for batch correction. Chevreul enables exploratory analyses of scRNA-seq data using Bioconductor SingleCellExperiment objects (or converted Seurat objects), including batch integration, quality control filtering, read count normalization and transformation, dimensionality reduction, clustering at a range of resolutions, and cluster marker gene identification. Processed data can be visualized in the R Shiny app. Gene or transcript expression can be visualized using PCA, tSNE, UMAP, heatmaps, or violin plots; differential expression can be evaluated with several statistical tests. Chevreul also provides accessible tools for isoform-level analyses and alternative splicing detection. Chevreul empowers researchers without programming experience to analyze full-length scRNA-seq data.
AVAILABILITY & IMPLEMENTATION: Chevreul is implemented in R, and the R package and integrated Shiny application are freely available at https://github.com/cobriniklab/chevreul with constituent packages hosted on Bioconductor at https://bioconductor.org/packages/chevreulProcess, https://bioconductor.org/packages/chevreulPlot, and https://bioconductor.org/packages/chevreulShiny.
Chevreul是一个用于处理和可视化单细胞RNA测序（scRNA-seq）数据的开源R语言Bioconductor软件包和交互式R Shiny应用程序。Chevreul在易用性、分析全长RNA测序数据以进行外显子覆盖和转录本异构体推断的能力以及对批次校正的支持方面与其他scRNA-seq分析软件包有所不同。Chevreul能够使用Bioconductor SingleCellExperiment对象（或转换后的Seurat对象）对scRNA-seq数据进行探索性分析，包括批次整合、质量控制过滤、读取计数归一化和转换、降维、在一系列分辨率下进行聚类以及聚类标记基因识别。处理后的数据可以在R Shiny应用程序中可视化。基因或转录本表达可以使用主成分分析（PCA）、t分布随机邻域嵌入（tSNE）、均匀流形近似和投影（UMAP）、热图或小提琴图进行可视化；差异表达可以通过几种统计测试进行评估。Chevreul还提供了用于异构体水平分析和可变剪接检测的便捷工具。Chevreul使没有编程经验的研究人员能够分析全长scRNA-seq数据。
Chevreul用R语言实现，其R软件包和集成的Shiny应用程序可在https://github.com/cobriniklab/chevreul免费获取，其组成软件包托管在Bioconductor上，网址分别为https://bioconductor.org/packages/chevreulProcess、https://bioconductor.org/packages/chevreulPlot和https://bioconductor.org/packages/chevreulShiny。
