For Single-cell analysis, there is a nice one https://www.nygen.io (paid plan) with visualization and analysis. For metabolics, there is MetaboAnalyst (https://www.metaboanalyst.ca) which is free online and R coded versions. There are few tools available for bulk RNA, spatial and proteomics but I don't remember something with GUI. Would be happy to know from others.

For bulk RNA-seq analysis several excellent tools are available:

- QIAGEN Ingenuity Pathway Analysis (IPA) (paid plan)- A comprehensive analysis platform ( https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-ipa/)

- These software: g:Profiler, Gene Set Enrichment Analysis (GSEA), Cytoscape and EnrichmentMap (Open-Access Tools) ( https://www.nature.com/articles/s41596-018-0103-9)

-clusterProfiler (R package) (https://www.sciencedirect.com/science/article/pii/S2666675821000667)

These tools support robust and insightful interpretation of bulk RNA-seq data. enabling identification of altered pathways and processes.

I'm not sure if you're looking for software that supports all of those data types in one platform, or tools that support each individually. If it's the former, there are some commercial options like DNAnexus—though from what I’ve seen, it's mainly geared towards genomics and transcriptomics. I haven't come across support for spatial data there yet, and the pricing might be a bit steep for labs with tighter budgets. My lab recently tested the C-DIAM platform from Pythia Biosciences (https://pythiabio.com), and it performed quite well. It supports all the data types you mentioned, and I especially liked its support for Visium HD, which is something our group is actively working with.