Empowering biologists to decode omics data: the Genekitr R package and web server

BMC Bioinformatics

Software

Gang Li¹  Yunze Liu¹ 

[1] Ministry of Education Frontiers Science Center for Precision Oncology, Faculty of Health Sciences, University of Macau, Macau SAR, China;Cancer Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China;Department of Biomedical Science, Faculty of Health Sciences, University of Macau, Macau SAR, China;

关键词: Bioinformatics tool;    Web server;    Gene set enrichment analysis;    Non-programming bioinformatics;    Plotting;   

DOI  :  10.1186/s12859-023-05342-9

 received in 2023-02-16, accepted in 2023-05-16,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundA variety of high-throughput analyses, such as transcriptome, proteome, and metabolome analysis, have been developed, producing unprecedented amounts of omics data. These studies generate large gene lists, of which the biological significance shall be deeply understood. However, manually interpreting these lists is difficult, especially for non-bioinformatics-savvy scientists.ResultsWe developed an R package and a corresponding web server—Genekitr, to assist biologists in exploring large gene sets. Genekitr comprises four modules: gene information retrieval, ID (identifier) conversion, enrichment analysis and publication-ready plotting. Currently, the information retrieval module can retrieve information on up to 23 attributes for genes of 317 organisms. The ID conversion module assists in ID-mapping of genes, probes, proteins, and aliases. The enrichment analysis module organizes 315 gene set libraries in different biological contexts by over-representation analysis and gene set enrichment analysis. The plotting module performs customizable and high-quality illustrations that can be used directly in presentations or publications.ConclusionsThis web server tool will make bioinformatics more accessible to scientists who might not have programming expertise, allowing them to perform bioinformatics tasks without coding.

【 授权许可】

CC BY   
© The Author(s) 2023

【 图 表 】

41116_2023_36_Article_IEq149.gif

41116_2023_36_Article_IEq146.gif

Fig. 1

41116_2023_36_Article_IEq145.gif

Fig. 1

41116_2023_36_Article_IEq143.gif

41116_2023_36_Article_IEq142.gif

Fig. 5

41116_2023_36_Article_IEq137.gif

40517_2023_256_Article_IEq58.gif