Difference between revisions of "Software"

Latest revision as of 01:03, 3 November 2025

[edit] CODE and DATABASE in Central Repositories

• Netbiolab GitHub site

[edit] 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

[edit] 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.

[edit] 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)

[edit] Functional Gene Networks

[edit] Animals

Mus musculus	Danio rerio	Drosophila melanogaster	Caenorhabditis elegans

[edit] Plants

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

[edit] Fungi

Saccharomyces cerevisiae	Cryptococcus neoformans

[edit] 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)

[edit] Build your own Functional gene networks

BiomeNet: A database for construction and analysis of functional interaction networks for any species with a sequenced genome

[edit] Network-augmented GWAS Analysis for Arabidopsis

araGWAB: genome-wide association boosting for Arabidopsis thaliana

[edit] Domain-based PPI networks by Weighted Mutual Information (WMI)

Project Page

[edit] Domain2Pathway by Pathway Specificity (PS)

Project Page