RT Journal Article
SR Electronic
T1 ALTRE: workflow for defining ALTered Regulatory Elements using chromatin accessibility data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 080564
DO 10.1101/080564
A1 Elizabeth Baskin
A1 Rick Farouni
A1 Ewy A. Mathe
YR 2016
UL http://biorxiv.org/content/early/2016/10/14/080564.abstract
AB 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 https://github.com/Mathelab/ALTREContact ewy.mathe{at}osumc.edu