getENRICH: a tool for the gene and pathway enrichment analysis of non-model organisms.

IF 2.4 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY

Bioinformatics advances Pub Date : 2025-02-07 eCollection Date: 2025-01-01 DOI:10.1093/bioadv/vbaf023

Ajay Bhatia, Pranjal Pruthi, Isha Chakraborty, Nityendra Shukla, Jitendra Narayan

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引用次数: 0

Abstract

Motivation: The Gene Ontology system facilitates the functional annotation of genes by categorizing them into specific biological processes, cellular components, and molecular functions. Despite numerous tools like DAVID and Enrichr, analysing non-model organisms remains challenging due to a lack of genetic information and available tools.

Results: To address this, we present getENRICH, a comprehensive tool for gene enrichment analysis tailored for non-model organisms. Available in both command-line and web-based graphical user interface (GUI) formats, getENRICH facilitates user-friendly interaction for gene dataset uploads, parameter configuration, and visualization. getENRICH employs hypergeometric distribution for P-value calculation and Benjamini-Hochberg correction for multiple testing.

Availability and implementation: getENRICH is freely available under the MIT license, with the source code, documentation, and example datasets available on GitHub (https://github.com/jnarayan81/getENRICH) and the GUI version available at https://getenrich.igib.res.in/.

查看原文本刊更多论文

getENRICH：非模式生物基因和途径富集分析工具。

动机：基因本体系统通过将基因分类为特定的生物过程、细胞成分和分子功能，促进了基因的功能注释。尽管有许多工具，如DAVID和enrichment，但由于缺乏遗传信息和可用工具，分析非模式生物仍然具有挑战性。结果：为了解决这个问题，我们提出了getENRICH，一个针对非模式生物量身定制的基因富集分析综合工具。getENRICH以命令行和基于web的图形用户界面（GUI）格式提供，有助于基因数据集上传，参数配置和可视化的用户友好交互。getENRICH采用超几何分布进行p值计算，采用Benjamini-Hochberg修正进行多重检验。可用性和实现：getENRICH在MIT许可下免费提供，其源代码、文档和示例数据集可在GitHub （https://github.com/jnarayan81/getENRICH）上获得，GUI版本可在https://getenrich.igib.res.in/上获得。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Bioinformatics advances

CiteScore

1.60

自引率

0.00%

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