vissE.cloud: a webserver to visualise higher order molecular phenotypes from enrichment analysis

Gene-set analysis (GSA) dominates the functional interpretation of omics data and downstream hypothesis generation. Despite its ability to summarise thousands of measurements into semantically interpretable components, GSA often results in hundreds of significantly enriched gene-sets. However, summarisation and effective visualisation of GSA results to facilitate hypothesis generation is still lacking. While some webservers provide gene-set visualiza-tion tools, there is still a need for tools that can effectively summarize and guide exploration of GSA results. To enable versatility, webservers accept gene lists as input, however, none provide end-to-end solutions for emerging data types such as single-cell and spatial omics. Here, we present vissE.Cloud, a webserver for end-to-end gene-set analysis, offering gene-set summarisation and highly interactive visu-alisation. vissE.Cloud uses algorithms from our ear-lier R package vissE to summarise GSA results by identifying biological themes. We maintain versatility by allowing analysis of gene lists, as well as, analy-sis of raw single-cell and spatial omics data, includ-ing CosMx and Xenium data, making vissE.Cloud the first webserver to provide end-to-end gene-set analysis of sub-cellular localised spatial data. Struc-turing the results hierarchically allows swift interac-tive investigations of results at the gene, gene-set, and clusters level. vissE.Cloud is freely available at https://www.vissE.Cloud. [GRAPHICS]