Welcome to scRNAbox's documentation!

ScRNAbox is a single-cell RNA sequencing (scRNAseq) pipeline specifically designed for analyzing data under a High-Performance Computing (HPC) systems using the Slurm Workload Manager. The scRNAbox pipeline leverages the Seurat v4 framework and incorporates eight analytical steps into a comprehensive scRNAseq analysis that provides the foundation for further investigations. The eight analytical steps are outlined below.

The scRNAbox pipeline provides two distinct, yet highly comparable analysis tracks:

  1. Standard analysis track
  2. HTO analysis track

The standard analysis track is designed for experiments where each sample is captured and sequenced separately, while the HTO analysis track is designed for multiplexed experiments where samples are tagged with sample-specific oligonucleotide tagged Hashtag antibodies (HTO), pooled, and sequenced together. The two tracks share all of the same processes except for Steps 1 and 4. In Step 1, the FASTQ processing for HTO data requires different configurations than the standard analysis. In Step 4, the HTO data is demultiplexed and a different doublet removal method is used.

For a comprehenseive description of each step, please see the Pipeline section of the scRNAbox documentation or see our pre-print manuscript.

For a tutorial that leverages the datasets used as the application cases in our pre-print manuscript, please see scRNAbox analysis of the midbrain dataset.

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