Software
Microbiome Data Analysis Tools
HRGM: Human reference gut microbiome of 5,414 prokaryotic species including newly assembled genomes from under-represented Asian metagenomes.
Single-cell Omics Data Analysis Tools
VirtualCytometry: A webserver for the study of immune cell differentiation using single-cell RNA sequencing data.
Network Medicine Tools
HumanNet: Human gene networks for disease research
TRRUST: Curated TF-target interaction networks in human and mouse
NGSEA: Network-augmented gene set enrichment analysis tool
MUFFINN: Cancer gene discovery via network analysis of somatic mutation data
GWAB: A web server for network-based boosting of human genome-wide association data
COEXPEDIA: Exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH)
MORPHIN: Network-assisted prediction of disease pathways in model organisms
RIDDLE: Network-assisted Gene Set Analysis (human only)
Co-functional Gene Networks
Laboratory Animals
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| Mus musculus | Danio rerio | Drosophila melanogaster | Caenorhabditis elegans |
Plants
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| Arabidopsis thaliana | Zea mays | Oryza sativa | Triticum aestivum | Hordeum vulgare | Glycine max | Solanum lycopersicum |
Fungi
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| Saccharomyces cerevisiae | Cryptococcus neoformans |
Bacteria
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| Pseudomonas aeruginosa (human pathogen) | Methicillin-resistant Staphylococcus aureus (human pathogen) | Klebsiella pneumoniae (human pathogen) | Escherichia coli (popular lab/factory bacterial species) | Xanthomonas oryzae pv. oryzae (rice pathogen) |
Build your own co-functional networks
BiomeNet: A database for construction and analysis of functional interaction networks for any species with a sequenced genome
Network-augmented GWAS Analysis for Arabidopsis
araGWAB: genome-wide association boosting for Arabidopsis thaliana
Domain-based PPI networks by Weighted Mutual Information (WMI)
