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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>.
Getting started
Package overview
scaper-vignette-CytoSig
scaper-vignette-Reactome
Cytokine Activity Estimation using SCAPE (Single cell transcriptomics-level Cytokine Activity Prediction and Estimation): An Analysis using the CytoSig database.
Cytokine Activity Estimation using SCAPE (Single cell transcriptomics-level Cytokine Activity Prediction and Estimation): An Analysis using the Reactome database.
Browse package contents
Package details |
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| Author | H. Robert Frost [aut], Azka Javaid [aut, cre] |
| Maintainer | Azka Javaid <azka.javaid.gr@dartmouth.edu> |
| License | GPL (>= 2) |
| Version | 0.2.0 |
| Package repository | View on CRAN |
| Installation |
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