ScRNAbox: empowering single-cell RNA sequencing on high performance computing systems.

ABSTRACT:

Background

Single-cell RNA sequencing (scRNAseq) offers powerful insights, but the surge in sample sizes demands more computational power than local workstations can provide. Consequently, high-performance computing (HPC) systems have become imperative. Existing web apps designed to analyze scRNAseq data lack scalability and integration capabilities, while analysis packages demand coding expertise, hindering accessibility.

Results

In response, we introduce scRNAbox, an innovative scRNAseq analysis pipeline meticulously crafted for HPC systems. This end-to-end solution, executed via the SLURM workload manager, efficiently processes raw data from standard and Hashtag samples. It incorporates quality control filtering, sample integration, clustering, cluster annotation tools, a

SUBMITTER: Thomas RA 

PROVIDER: S-EPMC11443813 | biostudies-literature | 2024 Oct

REPOSITORIES: biostudies-literature