BASiCS workflow – a step-by-step analysis of expression variability using single cell RNA sequencing data

Cell-to-cell gene expression variability is an inherent feature of complex biological systems, such as immunity and development. Single-cell RNA sequencing is a powerful tool to quantify this heterogeneity, but it is prone to strong technical noise. Researchers at the University of Edinburgh describe a step-by-step computational workflow that uses the BASiCS Bioconductor package to robustly quantify expression variability within and between known groups of cells (such as experimental conditions or cell types). BASiCS uses an integrated framework for data normalisation, technical noise quantification and downstream analyses, propagating statistical uncertainty across these steps. Within a single seemingly homogeneous cell population, BASiCS can identify highly variable genes that exhibit strong heterogeneity as well as lowly variable genes with stable expression. BASiCS also uses a probabilistic decision rule to identify changes in expression variability between cell populations, whilst avoiding confounding effects related to differences in technical noise or in overall abundance. Using a publicly available dataset, the researchers guide users through a complete pipeline that includes preliminary steps for quality control, as well as data exploration using the scater and scran Bioconductor packages. The workflow is accompanied by a Docker image that ensures the reproducibility of the results.

Graphical overview for the single cell RNA sequencing analysis workflow

Starting from a matrix of expression counts, we use the scater and scran Bioconductor packages to perform QC and initial exploratory analyses. To robustly quantify transcriptional heterogeneity within seemingly homogeneous cell populations, we apply the BASiCS Bioconductor package and illustrate how BASiCS can be used to analyse a single or multiple pre-specified groups of cells.

Availability – The source code for BASiCS, along with facilities contributing and reporting bugs is available at:

O’Callaghan A, Eling N, Marioni JC, Vallejos CA. (2022) BASiCS workflow: a step-by-step analysis of expression variability using single cell RNA sequencing data. F1000Research [Epub ahead of print]. [article]

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