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 <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, eval=FALSE}
# CRAN mirror
install.packages("cinaR")
```
### 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")
```

### Known Installation Issues

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

```{r, eval=FALSE}
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"))
```

## Usage

```{r setup, include=FALSE}
knitr::opts_chunk$set(dpi=300,fig.width=6)
```

```{r}
library(cinaR)

# create contrast vector which will be compared.
contrasts<- c("B6", "B6", "B6", "B6", "B6", "NZO", "NZO", "NZO", "NZO", "NZO", "NZO", 
              "B6", "B6", "B6", "B6", "B6", "NZO", "NZO", "NZO", "NZO", "NZO", "NZO")

# If reference genome is not set hg38 will be used!
results <- cinaR(bed, contrasts, reference.genome = "mm10")

pca_plot(results, contrasts, show.names = F)
```

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


## Citation
```
@article {Karakaslar2021.03.05.434143,
	author = {Karakaslar, E Onur and Ucar, Duygu},
	title = {cinaR: A comprehensive R package for the differential analyses and 
	functional interpretation of ATAC-seq data},
	year = {2021},
	doi = {10.1101/2021.03.05.434143},
	publisher = {Cold Spring Harbor Laboratory},
	URL = {https://www.biorxiv.org/content/early/2021/03/08/2021.03.05.434143.1},
	journal = {bioRxiv}
}
```

## Contribution

You can send pull requests to make your contributions.

## License

- GNU General Public License v3.0