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>.
| Version: | 0.2.0 |
| Depends: | R (≥ 3.5.0) |
| Imports: | magrittr,xml2,stringr,dplyr,Seurat,SeuratObject,VAM, utils |
| Suggests: | knitr,pheatmap,rmarkdown,usethis |
| Published: | 2025-04-16 |
| DOI: | 10.32614/CRAN.package.scaper |
| Author: | H. Robert Frost [aut], Azka Javaid [aut, cre] |
| Maintainer: | Azka Javaid <azka.javaid.gr at dartmouth.edu> |
| License: | GPL-2 |GPL-3 [expanded from: GPL (≥ 2)] |
| NeedsCompilation: | no |
| CRAN checks: | scaper results |
| Reference manual: | scaper.html ,scaper.pdf |
| Vignettes: | scaper-vignette-CytoSig (source,R code) scaper-vignette-Reactome (source,R code) |
| Package source: | scaper_0.2.0.tar.gz |
| Windows binaries: | r-devel:scaper_0.2.0.zip, r-release:scaper_0.2.0.zip, r-oldrel:scaper_0.2.0.zip |
| macOS binaries: | r-release (arm64):scaper_0.2.0.tgz, r-oldrel (arm64):scaper_0.2.0.tgz, r-release (x86_64):scaper_0.2.0.tgz, r-oldrel (x86_64):scaper_0.2.0.tgz |
| Old sources: | scaper archive |
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