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

E Onur Karakaslar, Duygu Ucar
doi: https://doi.org/10.1101/2021.03.05.434143
E Onur Karakaslar
1The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
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  • For correspondence: duygu.ucar@jax.org
Duygu Ucar
1The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
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  • For correspondence: duygu.ucar@jax.org
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Abstract

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

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Contact: onur.karakaslar{at}jax.org or duygu.ucar{at}jax.org

  • Typo in the manuscript title

  • https://CRAN.R-project.org/package=cinaR

  • https://CRAN.R-project.org/package=cinaRgenesets

  • https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE165120

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted March 08, 2021.
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cinaR: A comprehensive R package for the differential analyses and functional interpretation of ATAC-seq data
E Onur Karakaslar, Duygu Ucar
bioRxiv 2021.03.05.434143; doi: https://doi.org/10.1101/2021.03.05.434143
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cinaR: A comprehensive R package for the differential analyses and functional interpretation of ATAC-seq data
E Onur Karakaslar, Duygu Ucar
bioRxiv 2021.03.05.434143; doi: https://doi.org/10.1101/2021.03.05.434143

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