Work

GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions

Year: 2023

Type: software-paper

Abstract: SUMMARY: GSEL is a computational framework for calculating the enrichment of signatures of diverse evolutionary forces in a set of genomic regions. GSEL can flexibly integrate any sequence-based evolutionary metric and analyze sets of human genomic regions identified by genome-wide assays (e.g. GWAS, eQTL, *-seq). The core of GSEL's approach is the generation of empirical null distributions tailored to the allele frequency and linkage disequilibrium structure of the regions of interest. We illustrate the application of GSEL to variants identified from a GWAS of body mass index, a highly polygenic trait. AVAILABILITY AND IMPLEMENTATION: GSEL is implemented as a fast, flexible and user-friendly python package. It is available with demonstration data at https://github.com/abraham-abin13/gsel_vec. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Source: Bioinformatics

DOI: 10.1093/bioinformatics/btad037

Authors: Abin Abraham, Abigail L Labella, Mary Lauren Benton, Antonis Rokas, John A Capra

Institutions: Children's Hospital of Philadelphia, University of North Carolina at Charlotte, Vanderbilt University, Baylor University, University of California, San Francisco

Language: English

Topic: Genetic Associations and Epidemiology

Subfield: Genetics

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $3,618