README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/",
  out.width = "100%",
  fig.dpi = 96
)
```

# cinaR-genesets <a href='https://eonurk.github.io/cinaR/'><img src='man/figures/cinaR.png' align="right" height="139" /></a>


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[![CRAN version](https://www.r-pkg.org/badges/version/cinaRgenesets)](https://cran.r-project.org/package=cinaRgenesets)
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## Installation

```{r, eval=FALSE}
# CRAN mirror
install.packages("cinaRgenesets")
```

### Development Version
To get bug fix and use a feature from the development version:
```{r, eval=FALSE}
# install.packages("devtools")
devtools::install_github("eonurk/cinaR-genesets")
```

## Usage
You can use these modules via setting `geneset` argument in [cinaR](https://eonurk.github.io/cinaR/):
```{r eval = FALSE}
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)](https://doi.org/10.1038/s41467-020-14396-9)
```{r, eval=FALSE}
data("VP2008")
```

#### PBMC scRNAseq Modules
Curated from PBMC scRNA-seq data published in [here](https://www.nature.com/articles/s41590-020-0743-0):
```{r, eval=FALSE}
data("PBMC.scRNAseq")
```

#### Wikipathways
These genesets are curated from [wikipathways](https://www.wikipathways.org/index.php/WikiPathways):
```{r, eval=FALSE}
data("wiki")
```

#### Wikipathways Immune
Hand-picked subset of immune related pathways from [wikipathways](https://www.wikipathways.org/index.php/WikiPathways):
```{r, eval=FALSE}
data("wiki.immune")
```

#### Dice Major Cell Types
Major cell types curated from [DICE](https://www.dice-database.org/) database:
```{r, eval=FALSE}
data("dice.major")
```

#### Activated Immune Cells
Activated immune cells curated by [Ucarlab](https://www.ucarlab.com/) and published in [here](https://www.biorxiv.org/content/10.1101/2020.12.23.424147v1.abstract):
```{r, eval=FALSE}
data("activated.immune")
```

## Contribution

You can send pull requests to make your contributions.

## Author

- [E Onur Karakaslar](https://eonurk.github.io/)

## License

- GNU General Public License v3.0