Celline: a flexible tool for one-step retrieval and integrative analysis of public single-cell RNA sequencing data.

ABSTRACT: Single-cell RNA sequencing (scRNA-seq) has generated a rapidly expanding collection of public datasets that provide insight into development, disease, and therapy. However, researchers lack an end-to-end solution for seamlessly retrieving, preprocessing, integrating, and analyzing these data because existing tools address only isolated steps and require manual curation of accessions, metadata, and technical variability, known as batch effects. In this study, we developed Celline, a Python package that executes an entire workflow using a single-line commands per step. Celline automatically gathers raw single-cell RNA-seq data from multiple public repositories and extracts metadata using large language models. It then wraps established tools, including Scrublet for doublet removal, Seurat an

SUBMITTER: Sato Y 

PROVIDER: S-EPMC12738925 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature