This repository contains the code used to quantify and summarise individual RNA streams (computed using, e.g. velocyto) into a composite score that quantifies transition between two clusters. This is used in the following piece of work to evaluate the transition between different B cell subsets in a single-cell RNAseq dataset of peripheral B cells ('Pure' dataset).
The R markdown file contains all necessary functions to calculate and plot these estimates. Necessary input files for the 'Pure' dataset can be downloaded from ArrayExpress from here.
The associated publication is now on published in Frontiers In Immunology (previous version in bioRxiv). If you use it please cite:
Stewart AT, Ng J, Wallis G, Tsioligka V, Fraternali F & Dunn-Walters DK. (2021). Single-cell transcriptomic analyses define distinct peripheral B cell subsets and discrete development pathways. Frontiers In Immunology 12:743. doi: 10.3389/fimmu.2021.602539
Or as a BibTex format entry:
@ARTICLE{10.3389/fimmu.2021.602539,
AUTHOR={Stewart, Alexander and Ng, Joseph Chi-Fung and Wallis, Gillian and Tsioligka, Vasiliki and Fraternali, Franca and Dunn-Walters, Deborah K.},
TITLE={Single-Cell Transcriptomic Analyses Define Distinct Peripheral B Cell Subsets and Discrete Development Pathways},
JOURNAL={Frontiers in Immunology},
VOLUME={12},
PAGES={743},
YEAR={2021},
URL={https://www.frontiersin.org/article/10.3389/fimmu.2021.602539},
DOI={10.3389/fimmu.2021.602539},
ISSN={1664-3224},
}