Table 4.
Online tools for multi-omics integrative analysis.
| Tool | Description | Omics types | Website | PMID |
|---|---|---|---|---|
| LDexpress | It is an online tool that integrates population-specific linkage disequilibrium data and tissue-specific gene expression information to explore the impact of germline variation on nearby gene expression and disease associations. | Single nucleotide polymorphism, gene expression | https://ldlink.nih.gov/?tab=ldexpress | 34930111 (381) |
| Paintomics | It is a web server for multi-omics data analysis, offering improved pathway database support, enhanced metabolite analysis, and a regulatory omics module for comprehensive insights. | Transcriptomics, metabolomics | http://www.paintomics.org | 35609982 (382) |
| Quickomics | It empowers biologists with user-friendly modules, customizable options, and publication-ready visualizations for exploring and analyzing omics data with ease. | Transcriptomics, proteomics | http://quickomics.bxgenomics.com | 33901288 (383) |
| GeneTrail | It facilitates integrated analysis of various molecular datasets, including transcriptomic, miRNomic, genomic, and proteomic data, offering diverse statistical tests, reference sets, and biological categories while enabling direct result comparisons. | Genomics, transcriptomics, miRNomic, proteomics, epigenetics, single-cell omics | https://genetrail2.bioinf.uni-sb.de | 32379325 (384) |
| TIMEOR | It leverages ordered multi-omics data to reveal gene regulatory networks and mechanisms over time, offering researchers a valuable avenue for gaining insights into complex biological processes. | Genomics, transcriptomics, proteomics | http://timeor.brown.edu | 34125906 (385) |
| Omics Integrator | It is a powerful tool that utilizes network optimization algorithms to integrate multiple omic data types, revealing underlying molecular pathways and enabling the discovery of unannotated connections. | Proteomics, gene expression, epigenetics | http://fraenkel-nsf.csbi.mit.edu/omicsintegrator/ | 27096930 (386) |
| Mergeomics | It is a free online tool for integrating multi-omics data to reveal disease pathways, networks, key drivers, and potential drugs. | Genomics, epigenomics, transcriptomics, proteomics, metabolomics | http://mergeomics.research.idre.ucla.edu | 34048577 (387) |
| Online Resource for Integrative Omics (ORIO) | It is a web-based platform that enables intuitive and versatile analysis and integration of next-generation sequencing (NGS) data from various sources and techniques. | Genomics, epigenomics, transcriptomics, proteomics, metabolomics | https://orio.niehs.nih.gov/ | 28402545 (388) |
| GraphOmics | It is a user-friendly platform that integrates and explores multiple omics datasets by connecting biological entities based on biochemical relationships and mapping them to pathways. | Transcriptomics, proteomics, metabolomics | https://graphomics.glasgowcompbio.org/ | 34922446 (389) |
| 3Omics | It is a one-click web tool that streamlines the integration and analysis of transcriptomics, proteomics, and metabolomics data, providing visualizations and insights into relationships, functions, pathways, and enrichments across multiple omics datasets | Transcriptomics, proteomics, metabolomics | https://3omics.cmdm.tw/ | 23875761 (390) |
| MOVIS | It empowers researchers to efficiently explore time-series multi-omics data, creating valuable insights and reproducible visualizations with simplicity. | Diverse omics data | https://movis.mathematik.uni-marburg.de/ | 35284047 (391) |
| xMWAS | It is a versatile software that integrates, visualizes, clusters, and analyzes diverse omics data from multiple platforms, enabling the identification of sub-networks and topological changes in systems biology studies. | Diverse omics data | https://kuppal.shinyapps.io/xmwas/ | 29069296 (392) |
| OmicsNet | It enables researchers to visualize, analyze, and gain valuable insights from multi-omics data, fostering deeper understanding of complex biological systems. | Diverse omics data | www.omicsnet.ca | 35639733 (393) |
| MicrobioSee | It offers researchers an intuitive and efficient toolkit for visualizing complex multi-omics data and simplifying analysis. | Diverse omics data | https://microbiosee.gxu.edu.cn | 35464838 (394) |
| Visual Omics | It offers a seamless and intuitive solution for omics data analysis and visualization, enabling researchers to effortlessly generate customized and publication-ready charts that effectively communicate their findings. | Diverse omics data | http://bioinfo.ihb.ac.cn/visomics | 36458930 (395) |
| Interactive Data Explorer (OmicsTIDE) | It is a versatile bioinformatics tool designed to seamlessly integrate diverse numerical omics datasets, through concatenation and k-means clustering, enabling comprehensive multi-omics analysis and visualization of clustered associations. | Diverse omics data | http://omicstide-tuevis.cs.uni-tuebingen.de/ | 36698763 (396) |
| Galaxy | An open, web-based platform for data intensive biomedical research, which allows users to perform, reproduce, and share complete analyses. | Diverse omics data | https://usegalaxy.org/ | 35446428 (397) |