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Empowering biologists to decode omics data: the Genekitr R package and web server
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Empowering biologists to decode omics data: the Genekitr R package and web server
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Journal Article
Empowering biologists to decode omics data: the Genekitr R package and web server
2023
Overview
Background
A 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.
Results
We 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.
Conclusions
This web server tool will make bioinformatics more accessible to scientists who might not have programming expertise, allowing them to perform bioinformatics tasks without coding.
Publisher
BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
Subject
/ Biomedical and Life Sciences
/ Computational Biology/Bioinformatics
/ Computer Appl. in Life Sciences
/ Gene set enrichment analysis
/ Genes
/ Genomes
/ Genomics
/ Information Storage and Retrieval
/ Internet
/ Methods
/ Modules
/ Non-programming bioinformatics
/ Ontology
/ Plotting
/ Servers
/ Software
