scaper: Single Cell Transcriptomics-Level Cytokine Activity Prediction and Estimation

Generates cell-level cytokine activity estimates using relevant information from gene sets constructed with the 'CytoSig' and the 'Reactome' databases and scored using the modified 'Variance-adjusted Mahalanobis (VAM)' framework for single-cell RNA-sequencing (scRNA-seq) data. 'CytoSig' database is described in: Jiang at al., (2021) doi:10.1038/s41592-021-01274-5 . 'Reactome' database is described in: Gillespie et al., (2021) doi:10.1093/nar/gkab1028 . The 'VAM' method is outlined in: Frost (2020) doi:10.1093/nar/gkaa582 .

See also

Useful links:

• https://github.com/Zaoqu-Liu/scaper

• Report bugs at https://github.com/Zaoqu-Liu/scaper/issues

Author

Maintainer: Zaoqu Liu liuzaoqu@163.com

Authors:

• H. Robert Frost hildreth.r.frost@dartmouth.edu

• Azka Javaid azka.javaid.gr@dartmouth.edu