This repository consists of scripts and workflows used for generating results, figures, and tables published in the article: Rachel Sparks, William W. Lau, Can Liu, ..., John S. Tsang. "Influenza vaccination reveals sex dimorphic imprints of prior mild COVID-19". Nature (2023). https://www.nature.com/articles/s41586-022-05670-5
Please do the following in order to reproduce the figures shown in paper:
- download the Seurat object from GEO at https://ftp.ncbi.nlm.nih.gov/geo/series/GSE206nnn/GSE206265/suppl/GSE206265_covid_flu.CITEseq.Seurat.obj.RDS.gz and place the unpacked RDS file in the data folder
- download additional datasets on Zenodo at https://doi.org/10.5281/zenodo.5935844 (which resolves to the latest version of the upload) and place the files in the data folder
- for the Rmd file to compile, the project directory needs to be chosen as the knit directory
- follow any specific instructions on top of each script if provided
Please use the tables in the doc/figure.map.xlsx file to determine the code used for specific figures and their dependencies. Files generated by the scripts will be saved in the output folder that will be created automatically. Refer to the markdown reports in the docs folder for expected output.
By using this software, you agree this software is to be used for research purposes only. Any presentation of data analysis using the software will acknowledge the software according to the guidelines below.
Primary author(s): Rachel Sparks, William W. Lau, Can Liu, John S. Tsang
Organizational contact information: Rachel Sparks (rachel.sparks AT nih.gov)
Date of release: Jan 4, 2023
Version: 1.0
License details: see LICENSE file
Description: scripts used to generate figures and tables in the above publication
Usage instructions: Refer to README files in the specific folders
A review of this code has been conducted, no critical errors exist, and to the best of the authors knowledge, there are no problematic file paths, no local system configuration details, and no passwords or keys included in this code. This open source software comes as is with absolutely no warranty.