An immune-cell signature of bacterial sepsis
This repository contains code for reproducing the key figures and results from the following manuscript: Reyes, M., Filbin, M.R., et al. An immune-cell signature of bacterial sepsis. Nature Medicine (2020). 10.1038/s41591-020-0752-4
To run the notebooks, the following data objects and auxilliary files need to be downloaded through a data access request from Broad DUOS :
- matrix_clustered.h5ad
- matrix_ms1_sort.h5ad
- matrix_bm.h5ad
- fc_abundance_table.csv
- clinical_data.csv
- ms1_sort_table.csv
- ms1_cNMF_usage.txt
The datasets are also available on the Single Cell Portal for secondary analysis and visualization:
For questions, please contact Miguel Reyes (msreyes@broadinstitute.org)