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scaper  

Single Cell Transcriptomics-Level Cytokine Activity Prediction and Estimation
View on CRAN: Click here


Download and install scaper package within the R console
Install from CRAN:
install.packages("scaper")

Install from Github:
library("remotes")
install_github("cran/scaper")

Install by package version:
library("remotes")
install_version("scaper", "0.1.0")



Attach the package and use:
library("scaper")
Maintained by
Azka Javaid
[Scholar Profile | Author Map]
First Published: 2023-10-19
Latest Update: 2023-10-19
Description:
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) . 'Reactome' database is described in: Gillespie et al., (2021) . The 'VAM' method is outlined in: Frost (2020) .
How to cite:
Azka Javaid (2023). scaper: Single Cell Transcriptomics-Level Cytokine Activity Prediction and Estimation. R package version 0.1.0, https://cran.r-project.org/web/packages/scaper. Accessed 29 Mar. 2025.
Previous versions and publish date:
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Complete documentation for scaper
Functions, R codes and Examples using the scaper R package
Some associated functions: genesetCytoSig . genesetReactome . pipe . scape . scapeForSeurat . scaper-package . supportedCytokines . 
Some associated R codes: genesetCytoSig.R . genesetReactome.R . globals.R . scape.R . scapeForSeurat.R . scaper-package.R . supportedCytokines.R . utils-pipe.R .  Full scaper package functions and examples
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