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

ABSTRACT: 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 ( ALT ered R egulatory E lements), 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.https://github.com/Mathelab/ALTRE.ewy.mathe@osumc.edu.Supplementary data are available at Bioinformatics online.

SUBMITTER: Baskin E

PROVIDER: S-EPMC5408819 | biostudies-other | 2017 Mar

REPOSITORIES: biostudies-other

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

Baskin Elizabeth E Farouni Rick R Mathé Ewy A EA

Bioinformatics (Oxford, England) 20170301 5

<h4>Summary</h4>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 ( ALT ered R egulatory ...[more]

PMID: 28011773

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