Software

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)

Laboratory Animals

Mus musculus	Danio rerio	Drosophila melanogaster	Caenorhabditis elegans

Plants

Arabidopsis thaliana	Zea mays	Oryza sativa	Triticum aestivum	Glycine max	Solanum lycopersicum

Fungi

Saccharomyces cerevisiae	Cryptococcus neoformans

Bacteria

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)

Project Page

Domain2Pathway by Pathway Specificity (PS)

Project Page