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

ATAC-seq is a frequently used assay to study chromatin accessibility levels. Differential chromatin accessibility level 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, we are missing a stand-along R package that combines state-of-the art differential analyses and functional enrichment analyses. To fill this gap, we developed cinaR, which is a single wrapper function and provides users with various configurable plots. To show-case this pipeline we provide these bulk ATAC-seq samples from bone-marrow of 3 & 18 months old New Zelland Obese (NZO) mice and show the activation of pro-inflammatory pathways. Overall design: Bone marrow of NZO mice at 3 and 18 months