cinaR-genesets

Installation

# CRAN mirror
install.packages("cinaRgenesets")

Development Version

To get bug fix and use a feature from the development version:

# 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 6 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 in here:

data("PBMC.scRNAseq")

Wikipathways

These genesets are curated from wikipathways:

data("wiki")

Wikipathways Immune

Hand-picked subset of immune related pathways from wikipathways:

data("wiki.immune")

Dice Major Cell Types

Major cell types curated from DICE database:

data("dice.major")

Activated Immune Cells

Activated immune cells curated by Ucarlab and published in here:

data("activated.immune")

Contribution

You can send pull requests to make your contributions.

Author

• E Onur Karakaslar

License

• GNU General Public License v3.0