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>.

Version: 0.1.0
Depends: R (≥ 3.5.0)
Imports: magrittr, xml2, stringr, dplyr, Seurat, SeuratObject, VAM, utils
Suggests: knitr, pheatmap, rmarkdown, usethis
Published: 2023-10-19
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

Documentation:

Reference manual: scaper.pdf
Vignettes: scaper-vignette-CytoSig
scaper-vignette-Reactome

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Package source: scaper_0.1.0.tar.gz
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