[Preprint] cinaR: A comprehensive R package for the differential analyses and functional interpretation of ATAC-seq data

Published in bioaRxiv, 2021

Summary ATAC-seq is a frequently used assay to study chromatin accessibility levels. Differential chromatin accessibility analyses between biological groups and functional interpretation of these differential regions are essential in ATAC-seq data analyses. Although distinct methods and analyses pipelines are developed for this purpose, a stand-alone R package that combines state-of-the art differential and functional enrichment analyses pipelines is missing. To fill this gap, we developed cinaR (Chromatin Analyses in R), which is a single wrapper function and provides users with various data analyses and visualization options, including functional enrichment analyses with gene sets curated from multiple sources.

Availability and implementation cinaR is an R/CRAN package which is under GPL-3 License and its source code is freely accessible at https://CRAN.R-project.org/package=cinaR.

Gene sets are available at https://CRAN.R-project.org/package=cinaRgenesets.

Bone marrow ATAC-seq data is available at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE165120.

To cite, use the following bibtex entry:

@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},
	elocation-id = {2021.03.05.434143},
	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},
	eprint = {https://www.biorxiv.org/content/early/2021/03/08/2021.03.05.434143.1.full.pdf},
	journal = {bioRxiv}
}