peakScout - a biologist-friendly tool for bidirectional peak-gene mapping

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ID: 327787
2026
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Abstract
MOTIVATION: Translating genomic peak data into biologically meaningful knowledge typically requires bioinformatics expertise, creating a barrier for non-technical users. We developed peakScout to bridge the gap between peaks, genes and gene annotations, enabling users to quickly focus on biological context and not bioinformatics skills, in a reproducible and robust fashion. RESULTS: peakScout is a command line and web-based program that performs bidirectional mapping between genomic peaks and genes. The peak-to-gene mode identifies which genes are potentially regulated by specific genomic regions, while the gene-to-peak mode reveals which regulatory elements might influence particular genes of interest. An algorithm for nearest-feature detection handles the complex spatial relationships between genomic elements, considering factors like distance constraints and feature overlaps. AVAILABILITY: The web version of peakScout is available at https://vandydata.github.io/peakScout/. The command line version is available at https://github.com/vandydata/peakScout and archived on Zenodo (https://doi.org/10.5281/zenodo.21211605) under the GNU Affero General Public License v3.0. Installation instructions, example datasets, and usage examples are provided in the GitHub repository README file. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Reference Key
openalex_W7211912839 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Alexander L Lin, Lana A Cartailler, Jean‐Philippe Cartailler
Journal BMC Bioinformatics
Year 2026
DOI
10.1093/bioinformatics/btag653
URL
https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btag653/70984348/btag653.pdf
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