Here we explore the possibility of using scArches (Lotfollahi et al., 2020) to build a reference single-cell dataset of bronchoalveolar lavage (BAL) fluid from patients with COVID-19 and use it to analyse other BAL samples.
As reference dataset we used samples from COVID-positive patients from Grant et al., 2020 and as a query dataset we used COVID-negative samples from the same preprint. Both datasets have published cell type annotations which we used to assess scArches performance at capturing biological variability in its latent space and at predicting cell type labels.
All the analysis is here https://nbviewer.jupyter.org/github/NUPulmonary/scarches-covid-reference/blob/master/main.ipynb
Dependencies for this exploration are managed by pipenv
Acknoledgements
This analysis wouldn't have been possible without help from Mohammad Lotfollahi (https://github.com/M0hammadL), Alexander Misharin (https://github.com/amisharin) and
all the teams behind scArches project and Grant et al., 2020 preprint.