Reproducibility repository accompanying Wilk, Rustagi, Zhao, et al. "A single-cell atlas of the peripheral immune response in patients with severe COVID-19" Nature Medicine (2020).
You will find R and python scripts to download data and reproduce the analyses in the "code" folder.
Processed count matrices with de-identified metadata and embeddings are available for download from the Covid-19 Cell Atlas (https://www.covid19cellatlas.org/#wilk20) hosted by the Wellcome Sanger Institute. Processed data is also available for viewing and exploration on the publicly accessible cellxgene platform by the Chan Zuckerberg Initiative at https://cellxgene.cziscience.com/d/Single_cell_atlas_of_peripheral_immune_response_to_SARS_CoV_2_infection-25.cxg/. Raw sequencing data are available at the NCBI Gene Expression Omnibus (accession number GSE150728). Requests for additional materials can be made via email to the corresponding authors: Catherine A. Blish (cblish@stanford.edu) or Angela J. Rogers (ajrogers@stanford.edu).
Bam files are available here: https://drive.google.com/drive/folders/1qf62ip8WorEV-KLf_WSi8AMyyMoNdfln?usp=sharing
This repository is a work-in-progress and will be updated frequently!