Difference between revisions of "Software"
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[[File:TRRUST_logo.jpg |150px|link=//www.grnpedia.org/trrust/]] '''TRRUST''': Curated TF-target interaction networks in human and mouse | [[File:TRRUST_logo.jpg |150px|link=//www.grnpedia.org/trrust/]] '''TRRUST''': Curated TF-target interaction networks in human and mouse | ||
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| + | [[File:Coexpedia.png |150px|link=http://www.coexpedia.org]] '''COEXPEDIA''': Exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH) | ||
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[[File:GWAB_logo.png |150px|link=//www.inetbio.org/gwab]] '''GWAB''': A web server for network-based boosting of human genome-wide association data | [[File:GWAB_logo.png |150px|link=//www.inetbio.org/gwab]] '''GWAB''': A web server for network-based boosting of human genome-wide association data | ||
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[[File:Cover title riddle.jpg|150px|link=http://www.functionalnet.org/riddle]] '''RIDDLE''': Network-assisted Gene Set Analysis (human only) | [[File:Cover title riddle.jpg|150px|link=http://www.functionalnet.org/riddle]] '''RIDDLE''': Network-assisted Gene Set Analysis (human only) | ||
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=='''Co-functional Gene Networks'''== | =='''Co-functional Gene Networks'''== | ||
Revision as of 13:13, 6 June 2021
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
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)
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)
