ALTRE: workflow for defining ALTered Regulatory Elements using chromatin accessibility data

SUMMARY: Regulatory elements regulate gene transcription, and their location and accessibility is cell-type specific, particularly for enhancers. Mapping and comparing chromatin accessibility between different cell types may identify mechanisms involved in cellular development and disease progression. To streamline and simplify differential analysis of regulatory elements genome-wide using chromatin accessibility data, such as DNase-seq, ATAC-seq, we developed ALTRE (ALTered Regulatory Elements), an R package and associated R Shiny web app. ALTRE makes such analysis accessible to a wide range of users—from novice to practiced computational biologists. AVAILABILITY AND IMPLEMENTATION: https://github.com/Mathelab/ALTRE SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.