EISCA and EISTA: Full-Spectrum Pipelines for Single-Cell and Spatial Transcriptomics Analysis

Single-cell and spatial transcriptomics are revolutionizing our comprehension of cellular diversity and tissue structure; however, their analytical complexity poses a significant challenge. Introducing two comprehensive, end-to-end pipelines: EISCA and EISTA. Both pipelines, constructed on the Nextflow nf-core framework, offer modular, scalable, and reproducible workflows for single-cell RNA-seq and imaging-based spatial transcriptomics analysis, starting from raw data processing to advanced downstream analyses.

EISCA accommodates droplet- and plate-based scRNA-seq technologies, while EISTA is specifically designed for high-resolution spatial platforms such as Vizgen MERFISH and 10x Xenium. These pipelines combine cutting-edge techniques for quality control, normalization, clustering, integration, cell-type annotation, differential expression, and cell-cell communication. EISTA further enables spatial statistical analyses.

The core philosophy behind these pipelines is to strike a balance between standardization and flexibility, allowing users to execute workflows end-to-end or modularly, thus enabling iterative, exploratory analyses with minimal overhead. Upon completion, both pipelines provide rapid preliminary results and an out-of-the-box report, facilitating immediate data assessment and expediting downstream discovery.

Real-world applications of EISTA and EISCA have demonstrated their efficacy in plant immunity and human sepsis studies. These pipelines were able to consistently recover biologically meaningful insights. In summary, EISCA and EISTA offer efficient, flexible, and scalable solutions for comprehensive single-cell and spatial transcriptomics analyses.