scRNA-seq data on influenza infected human nasal wash samples

This repository contains scripts for the study on influenza virus infected human nasal wash samples using scRNA-seq:

Cao Y*, Guo Z*, Vangala P, Donnard E, Liu P, McDonel P, Ordovas-Montanes J, Finberg RW, Wang JW#, and Garber M# “Single cell analysis of upper airway cells reveals host and viral dynamics in influenza-infected adults.” bioRxiv.

The analysis highlights the algorithm scVirusFinder in defining infected cells in scRNA-seq data given ambient RNA contamination.
Scripts for index swapping and cell barcode collision for Seq-Well data sequenced on NovaSeq platform.