Difference between revisions of "Software"
From Bioinformatics Lab
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− | ==''' | + | =='''Network Medicine 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:Cover title muffinn.png |150px|link=http://www.inetbio.org/muffinn/]] '''MUFFINN''': Cancer gene discovery via network analysis of somatic mutation data | [[File:Cover title muffinn.png |150px|link=http://www.inetbio.org/muffinn/]] '''MUFFINN''': Cancer gene discovery via network analysis of somatic mutation 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 | [[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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− | + | =='''Co-functional Gene Networks'''== | |
− | =='''Co-functional | + | |
==''Human and Laboratory Animals''== | ==''Human and Laboratory Animals''== | ||
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==''Bacteria''== | ==''Bacteria''== | ||
{|border="0" width="200" | {|border="0" width="200" | ||
+ | |align="center"|[[File:Pseudomonas logo.jpg|150px|link=http://www.inetbio.org/pseudomonasnet]] | ||
|align="center"|[[File:Staphnet_logo.JPG|150px|link=http://www.inetbio.org/staphnet]] | |align="center"|[[File:Staphnet_logo.JPG|150px|link=http://www.inetbio.org/staphnet]] | ||
− | |align="center"|[[File: | + | |align="center"|[[File:KlebNet_logo.png|150px|link=http://www.inetbio.org/klebnet]] |
|align="center"|[[File:EcoliNet.png|150px|link=http://www.inetbio.org/ecolinet]] | |align="center"|[[File:EcoliNet.png|150px|link=http://www.inetbio.org/ecolinet]] | ||
|align="center"|[[File:XooNet_logo.png|150px|link=http://www.inetbio.org/xoonet]] | |align="center"|[[File:XooNet_logo.png|150px|link=http://www.inetbio.org/xoonet]] | ||
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− | |align="center"|Methicillin-resistant ''Staphylococcus aureus'' | + | |align="center"|''Pseudomonas aeruginosa (human pathogen)'' |
− | |align="center"|'' | + | |align="center"|Methicillin-resistant ''Staphylococcus aureus (human pathogen)'' |
− | |align="center"|''Escherichia coli'' | + | |align="center"|''Klebsiella pneumoniae (human pathogen)'' |
− | |align="center"|''Xanthomonas oryzae pv. oryzae'' | + | |align="center"|''Escherichia coli (popular lab/factory bacterial species)'' |
+ | |align="center"|''Xanthomonas oryzae pv. oryzae (rice pathogen)'' | ||
|} | |} | ||
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+ | =='''Network-augmented GWAS Analysis for Arabidopsis'''== | ||
+ | [[File:araGWAB_logo.png|150px|link=http://www.inetbio.org/aragwab]] | ||
+ | '''araGWAB''': genome-wide association boosting for ''Arabidopsis thaliana'' | ||
Revision as of 14:57, 23 February 2018
Network Medicine Tools
TRRUST: A reference database of TF-target interactions in human and mouse
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
Homo sapiens | 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
Build your own co-functional networks
JiffyNet: Instant gene network building server for newly sequenced species
Network-augmented GWAS Analysis for Arabidopsis
araGWAB: genome-wide association boosting for Arabidopsis thaliana
Domain-based PPI networks by Weighted Mutual Information (WMI)