Fig. 1. Schematic of scPipeline analysis modules.

a scPipeline is a modular collection of Rmarkdown scripts that generate reports for scRNA-seq analyses. The modular framework permits flexible usage and facilitates i) QC & preprocessing, ii) integration, iii) cluster optimization, iv) cell annotation, v) gene expression and association analyses, and vi) gene program discovery. Each standalone HTML report provides a comprehensive analysis summary that can be seamlessly shared without any dependencies. Alternatively, online repositories (e.g., GitHub) can be used to host HTML reports for public dissemination. b Representative snapshots of scPipeline reports generated using the QC and preprocessing (left), cell annotation (middle), and gene expression and association (right) modules. More examples can be found here.