Web Applications for Omics Analysis

This collection highlights web-based applications that complement command-line workflows and provide accessible interfaces for specialized analyses. These tools are particularly valuable for exploratory analysis, visualization, and when you need quick results without setting up complex software environments.

Web applications offer several advantages: no installation requirements, regular updates by developers, and often integrate multiple analysis steps into streamlined workflows. They’re ideal for pilot studies, method comparison, and sharing results with collaborators who may not have computational expertise.

However, web applications have significant limitations that researchers should consider: poor or unclear documentation of methods and usage, infrequent updates that leave tools outdated, limited reproducibility compared to command-line approaches, and often slow performance with large datasets. Additionally, many web tools lack version control, making it difficult to recreate analyses months or years later.

Given these trade-offs, we have curated a select few web applications that we’ve found to be well-maintained, documented, and useful for specific tasks. For critical analyses or publication-quality work, we recommend complementing web applications with reproducible command-line workflows.

The following categories organize web applications by their scope and intended use:

Integrated Analysis Platforms

Comprehensive web applications that provide end-to-end analysis workflows, from data upload through statistical analysis and visualization. These platforms handle multiple analysis types and are ideal when you want a complete solution in one interface.

Examples: ExpressAnalyst, iDEP, Galaxy

Specialized Analysis Tools

Focused applications that excel at specific analytical tasks such as pathway analysis, network visualization, or particular statistical methods. These tools offer deep functionality in their domain and often provide more sophisticated options than general platforms.

Examples: Enrichr, STRING, ClusterProfiler web interface, ComplexHeatmap Shiny

Public Data Exploration

Web applications designed for mining, visualizing, and analyzing publicly available omics datasets. These tools provide access to large data compendia and enable hypothesis generation through data exploration.

Examples: GREIN, GEPIA, cBioPortal, Expression Atlas

For guidance on integrating web application results with local analyses, see our sections on Data Import/Export and Reproducible Workflows.