Software

CODE and DATABASE in Central Repositories

• Netbiolab GitHub site
• Netbiolab HuggingFace site

Microbiome Research

HRGM: A Human Reference Gut Microbiome comprising 232,098 genomes for 5414 prokaryotic species and 103 million unique proteins

HROM: A Human Reference Oral Microbiome comprising 72,641 genomes for 3,426 prokaryotic species and 8.49 million unique proteins

MRGM: A Mouse Reference Gut Microbiome comprising 46,267 genomes for 1,689 bacterial species and 15.2 million proteins

MRGV: A Mouse Reference Gut Virome comprising 109,778 genomes for 28,824 species-level vOTUs and 1.3 million unique proteins

Single-cell Biology

scHumanNet: Cell-type-specific functional gene networks using single-cell RNA-sequencing data

VirtualCytometry: A webserver for the study of immune cell differentiation using single-cell RNA sequencing data.

Network Medicine

HumanNet: Human gene networks for disease research

TRRUST: Curated TF-target interaction networks in human and mouse

COEXPEDIA: Exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH)

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

MORPHIN: Network-assisted prediction of disease pathways in model organisms

RIDDLE: Network-assisted Gene Set Analysis (human only)

Animals

Mus musculus	Danio rerio	Drosophila melanogaster	Caenorhabditis elegans

Plants

Arabidopsis thaliana	Zea mays	Oryza sativa	Triticum aestivum	Hordeum vulgare	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 Functional gene 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