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cinaR

A differential and enrichment analyses pipeline for bulk ATAC-seq (and RNA-seq)

https://github.com/eonurk/cinar

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: biorxiv.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (20.1%) to scientific vocabulary

Keywords

atac-seq differential-analysis enrichment-analysis gene-sets
Last synced: 6 months ago · JSON representation

Repository

A differential and enrichment analyses pipeline for bulk ATAC-seq (and RNA-seq)

Basic Info
Statistics
  • Stars: 13
  • Watchers: 2
  • Forks: 3
  • Open Issues: 1
  • Releases: 0
Topics
atac-seq differential-analysis enrichment-analysis gene-sets
Created over 5 years ago · Last pushed almost 2 years ago
Metadata Files
Readme

README.Rmd 

---
output: github_document
---



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

# cinaR 



![RMD check](https://github.com/eonurk/cinaR/actions/workflows/R-CMD-check.yaml/badge.svg)
[![CRAN version](https://www.r-pkg.org/badges/version/cinaR)](https://cran.r-project.org/package=cinaR)
[![CRAN download](https://cranlogs.r-pkg.org/badges/cinaR?color=orange)](https://cran.r-project.org/package=cinaR?color=orange)


## 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

Owner

  • Name: Onur Karakaslar
  • Login: eonurk
  • Kind: user
  • Location: Leiden

Featuring random thoughts

GitHub Events

Total
  • Watch event: 3
Last Year
  • Watch event: 3

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 149
  • Total Committers: 6
  • Avg Commits per committer: 24.833
  • Development Distribution Score (DDS): 0.503
Top Committers
Name Email Commits
Onur Karakaslar k****o@M****e 74
Onur Karakaslar k****o@M****l 30
eonurk o****4@g****m 26
Onur Karakaslar k****o@m****t 7
Onur Karakaslar e****k@O****e 6
Onur Karakaslar k****o@m****g 6
Committer Domains (Top 20 + Academic)
mlg-jgm123.jax.org: 1 onurs-mbp.home: 1 mlg-jgm123.mynet: 1 mlg-jgm123.home: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 6
  • Total pull requests: 1
  • Average time to close issues: 6 days
  • Average time to close pull requests: over 1 year
  • Total issue authors: 4
  • Total pull request authors: 1
  • Average comments per issue: 2.5
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • eonurk (3)
  • alperoglu (1)
  • cmf1997 (1)
  • sngholee (1)
Pull Request Authors
  • alperoglu (2)
Top Labels
Issue Labels
enhancement (3)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 147 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 4
  • Total maintainers: 1
cran.r-project.org: cinaR

A Computational Pipeline for Bulk 'ATAC-Seq' Profiles

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 147 Last month
Rankings
Stargazers count: 17.0%
Forks count: 17.8%
Dependent packages count: 29.8%
Average: 33.0%
Dependent repos count: 35.5%
Downloads: 65.0%
Maintainers (1)
eonurkara@gmail.com
Last synced: 7 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.0.0 depends
  • ChIPseeker * imports
  • DESeq2 * imports
  • GenomicRanges * imports
  • RColorBrewer * imports
  • TxDb.Hsapiens.UCSC.hg19.knownGene * imports
  • TxDb.Hsapiens.UCSC.hg38.knownGene * imports
  • TxDb.Mmusculus.UCSC.mm10.knownGene * imports
  • dplyr * imports
  • edgeR * imports
  • fgsea * imports
  • ggplot2 * imports
  • ggrepel * imports
  • grDevices * imports
  • limma * imports
  • pheatmap * imports
  • preprocessCore * imports
  • sva * imports
  • utils * imports
  • writexl * imports
  • knitr * suggests
  • markdown * suggests
  • rmarkdown * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/setup-r v1 composite
.github/workflows/pkgdown.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite