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 incorporates nine Analytical Steps into a comprehensive scRNAseq analysis and provides the foundation for further investigations. The nine Analytical Steps are outlined below.

The scRNAbox pipeline provides two distinct, yet highly comparable Analysis Tracks:

  1. Standard scRNAseq
  2. Cell Hashtag scRNAseq

The Standard Analysis Track is designed for experiments where each sample is captured and sequenced separately, while the Cell Hashtag Analysis Track is designed for multiplexed experiments, whereby samples are tagged with sample-specific barcodes, pooled, and sequenced together. The Cell Hashtag Analysis Track is distinguished by an additional sample demultiplexing Step that assigns cells to their sample-of-origin via the sample-specific barcodes.

For a comprehenseive description of each Analytical Step, please see Standard Analysis Track and Cell Hashtag Analysis Track.

For a tutorial that leverages the datasets used as the application cases in our pre-print manuscript, please see Standard Analysis: Midbrain dataset and Cell Hashtag Analysis: PBMC dataset.


Contents