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

Abstract

SummaryATAC-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 implementationcinaR 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 Contactonur.karakaslar@jax.org or duygu.ucar@jax.org