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

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## Overview

`cinaR` is a single wrapper function for end-to-end computational
analyses of bulk ATAC-seq (or RNA-seq) profiles. Starting from a
consensus peak file, it outputs differentially accessible peaks,
enrichment results, and provides users with various configurable
visualization options. For more details, please see the
[preprint](https://www.biorxiv.org/content/10.1101/2021.03.05.434143v2).

![](man/figures/overview@5x.png)

## Installation

``` r
# CRAN mirror
install.packages("cinaR")
```

### Development version

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

``` r
# install.packages("devtools")
devtools::install_github("eonurk/cinaR")
```

## Usage

For more details please go to our site from
[here!](https://eonurk.github.io/cinaR/articles/cinaR.html)

### Known Installation Issues

Sometimes bioconductor related packages may not be installed
automatically.  
Therefore, you may need to install them manually:

``` r
BiocManager::install(c("ChIPseeker", "DESeq2", "edgeR", "fgsea","GenomicRanges", "limma", "preprocessCore", "sva", "TxDb.Hsapiens.UCSC.hg38.knownGene", "TxDb.Hsapiens.UCSC.hg19.knownGene", "TxDb.Mmusculus.UCSC.mm10.knownGene"))
```

## 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
