Difference between revisions of "Software"
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=='''Gene Regulation Research Tools'''== | =='''Gene Regulation Research Tools'''== | ||
[[File:TRRUST_logo.jpg |150px|link=http://www.grnpedia.org/trrust/]] '''TRRUST''': A reference database of TF-target interactions in human and mouse | [[File:TRRUST_logo.jpg |150px|link=http://www.grnpedia.org/trrust/]] '''TRRUST''': A reference database of TF-target interactions in human and mouse | ||
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[[File:GWAB_logo.png |150px|link=http://www.inetbio.org/gwab]] '''GWAB''': A web server for network-based boosting of human genome-wide association data | [[File:GWAB_logo.png |150px|link=http://www.inetbio.org/gwab]] '''GWAB''': A web server for network-based boosting of human genome-wide association data | ||
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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) | [[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:Logo morphin.png|150px|link=http://www.inetbio.org/morphin/]] '''MORPHIN''': Network-assisted prediction of disease pathways in model organisms | [[File:Logo morphin.png|150px|link=http://www.inetbio.org/morphin/]] '''MORPHIN''': Network-assisted prediction of disease pathways in model organisms | ||
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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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| + | =='''Plant GWAS Analysis'''== | ||
| + | [[File:araGWAB_logo.png|150px|link=http://www.inetbio.org/aragwab]] | ||
| + | '''araGWAB''': genome-wide association boosting for ''Arabidopsis thaliana'' | ||
Revision as of 13:31, 25 January 2018
Gene Regulation Research Tools
TRRUST: A reference database of TF-target interactions in human and mouse
Network Medicine Tools
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
Human and Laboratory Animals
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| Homo sapiens | Mus musculus | Danio rerio | Drosophila melanogaster | Caenorhabditis elegans |
Plants
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| Arabidopsis thaliana | Zea mays | Oryza sativa | Triticum aestivum | 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
JiffyNet: Instant gene network building server for newly sequenced species
Plant GWAS Analysis
araGWAB: genome-wide association boosting for Arabidopsis thaliana
Domain-based PPI networks by Weighted Mutual Information (WMI)
