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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

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.