Ready-to-Use Curated Gene Sets for 'cinaR'

Immune related gene sets provided along with the 'cinaR' package.

cinaR-genesets

Installation

# install.packages("devtools")
devtools::install_github("eonurk/cinaR-genesets")

Usage

You can use these modules via setting geneset argument in cinaR:

library(cinaR)
library(cinaRgenesets)

data("VP2008")
cinaR(..., geneset = vp2008)

Available Genesets

This package contains 5 genesets curated from different sources.

Immune Modules

Immune system related modules from SLE patients published in Nature Communications (2020)

data("VP2008")

PBMC scRNAseq Modules

Curated from PBMC scRNA-seq data (published via cinaR):

data("PBMC.scRNAseq")

Wikipathways

These genesets are curated from wikipathways:

data("wiki")

Wikipathways Inflammation

Hand-picked subset of inflammation related pathways from wikipathways:

data("wiki.inf")

Dice Major Cell Types

Major cell types curated from DICE database

data("dice.major")

Contribution

You can send pull requests to make your contributions.

Author

• E Onur Karakaslar

License

• GNU General Public License v3.0