瓦兰托（Varanto）：变体富集分析和注释。

Varanto: variant enrichment analysis and annotation.

机构信息

Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland.

Institute of Biomedicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland.

出版信息

Bioinformatics. 2019 Sep 1;35(17):3154-3156. doi: 10.1093/bioinformatics/btz046.

DOI:10.1093/bioinformatics/btz046

PMID:30689722

Abstract

SUMMARY

Genome-wide association studies (GWAS) aim to identify associations of genetic variations such as single-nucleotide polymorphisms (SNPs) to a specific trait or a disease. Identifying common themes such as pathways, biological processes and diseases associations is needed to further explore and interpret these results. Varanto is a novel web tool for annotating, visualizing and analyzing human genetic variations using diverse data sources. Varanto can be used to query a set of input variations, retrieve their associated variation and gene level annotations, perform annotation enrichment analysis and visualize the results.

AVAILABILITY AND IMPLEMENTATION

Varanto web app is developed with R and implemented as Shiny app with PostgreSQL database and is freely available at http://bioinformatics.uef.fi/varanto. Source code for the tool is available at https://github.com/oqe/varanto.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

全基因组关联研究（GWAS）旨在识别遗传变异（如单核苷酸多态性 [SNP]）与特定特征或疾病之间的关联。需要确定途径、生物过程和疾病关联等常见主题，以进一步探索和解释这些结果。Varanto 是一种新颖的网络工具，用于使用各种数据源注释、可视化和分析人类遗传变异。Varanto 可用于查询一组输入变异，检索它们相关的变异和基因水平注释，执行注释富集分析并可视化结果。

可用性和实现

Varanto 网络应用程序是使用 R 开发的，并作为 Shiny 应用程序实现，使用 PostgreSQL 数据库，可在 http://bioinformatics.uef.fi/varanto 上免费获得。该工具的源代码可在 https://github.com/oqe/varanto 上获得。