The scPipeline analysis pipeline is a modular collection of R markdown scripts that generate flexdashboard reports for scRNAseq analyses, and is dependent on the scMiko package. The modular framework permits flexible usage, without necessitating complete reliance on a single analysis platform. Additionally, the self-contained reports that are generated by each module provide a comprehensive analysis summary and log of analytic parameters and scripts, thereby ensuring reproducible and shareable analysis workflows.
To get started with scPipeline, please refer to our scMiko and scPipeline tutorials.
if using scPipeline and scMiko, please consider citing our work: Mikolajewicz, et al., BioRxiv