scRNAbox

scRNAbox executes an end-to-end single-cell RNA sequencing analysis pipeline on high-performance computing systems using the Slurm workload manager.

Key Features:

• Quality Control Filtering: scRNAbox incorporates quality control filtering of raw single-cell RNA sequencing data.
• Sample Integration: scRNAbox performs sample integration for combining multiple datasets.
• Clustering: scRNAbox performs clustering analysis of single-cell transcriptomic data.
• Cluster Annotation: scRNAbox provides cluster annotation tools for identifying cell types.
• Differential Gene Expression Analysis: scRNAbox facilitates cell type-specific differential gene expression analysis between two groups.
• Standard and Hashtag Sample Processing: scRNAbox efficiently processes raw data from standard and Hashtag samples.

Scientific Applications:

• Large-Scale scRNAseq Analysis: scRNAbox addresses the computational demands of analyzing large sample sizes that exceed local workstation capabilities.
• Cell Type-Specific Comparative Analysis: scRNAbox enables comparison of gene expression between experimental groups at the cell type level.

Methodology:

scRNAbox is executed via the SLURM workload manager on high-performance computing systems.