Difference between revisions of "Software"

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__NOTOC__
 
__NOTOC__
=='''Gene Regulation Research Tools'''==
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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
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[[File:HumanNet_logo_with_title.png|150px|link=http://www.inetbio.org/humannet]]'''HumanNet''': Human gene networks for disease research
  
  
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[[File:TRRUST_logo.jpg |150px|link=http://www.grnpedia.org/trrust/]] '''TRRUST''': Curated TF-target interaction networks 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
=='''Network Medicine Tools '''==
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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:Cover title muffinn.png |150px|link=http://www.inetbio.org/muffinn/]] '''MUFFINN''': Cancer gene discovery via network analysis of somatic mutation 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)
 
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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
 
  
  
 
[[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'''==
  
 
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==''Laboratory Animals''==
 
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{|border="0"  width="400"
 
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=='''Co-functional gene networks'''==
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==''Human and Laboratory Animals''==
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{|border="0"  width="500"
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|align="center"|[[file:Tools_HumanNetLogo.jpg|150px|link=http://www.functionalnet.org/humannet]]
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|align="center"|[[file:MouseNetLogo.png|150px|link=http://www.inetbio.org/mousenet]]
 
|align="center"|[[file:MouseNetLogo.png|150px|link=http://www.inetbio.org/mousenet]]
 
|align="center"|[[file:danionet_logo.png|150px|link=http://www.inetbio.org/danionet]]
 
|align="center"|[[file:danionet_logo.png|150px|link=http://www.inetbio.org/danionet]]
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|align="center"|[[file:WormNetv3.jpg|150px|link=http://www.inetbio.org/wormnet]]
 
|align="center"|[[file:WormNetv3.jpg|150px|link=http://www.inetbio.org/wormnet]]
 
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|align="center"|''Homo sapiens''
 
 
|align="center"|''Mus musculus''
 
|align="center"|''Mus musculus''
 
|align="center"|''Danio rerio''
 
|align="center"|''Danio rerio''
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==''Bacteria''==
 
==''Bacteria''==
 
{|border="0"  width="200"
 
{|border="0"  width="200"
|align="center"|[[File:Staphnet_logo.JPG|150px|link=http://www.inetbio.org/staphnet]]
 
 
|align="center"|[[File:Pseudomonas logo.jpg|150px|link=http://www.inetbio.org/pseudomonasnet]]
 
|align="center"|[[File:Pseudomonas logo.jpg|150px|link=http://www.inetbio.org/pseudomonasnet]]
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|align="center"|[[File:Staphnet_logo.JPG|150px|link=http://www.inetbio.org/staphnet]]
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|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''
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|align="center"|''Pseudomonas aeruginosa (human pathogen)''
|align="center"|''Pseudomonas aeruginosa''
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|align="center"|Methicillin-resistant ''Staphylococcus aureus (human pathogen)''
|align="center"|''Escherichia coli''
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|align="center"|''Klebsiella pneumoniae (human pathogen)''
|align="center"|''Xanthomonas oryzae pv. oryzae''
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|align="center"|''Escherichia coli (popular lab/factory bacterial species)''
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|align="center"|''Xanthomonas oryzae pv. oryzae (rice pathogen)''
 
|}
 
|}
  
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=='''Network-augmented GWAS Analysis for Arabidopsis'''==
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[[File:araGWAB_logo.png|150px|link=http://www.inetbio.org/aragwab]]
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'''araGWAB''': genome-wide association boosting for ''Arabidopsis thaliana''
  
  

Revision as of 16:18, 13 August 2018

Network Medicine Tools

HumanNet logo with title.pngHumanNet: Human gene networks for disease research


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


Cover title muffinn.png MUFFINN: Cancer gene discovery via network analysis of somatic mutation data


GWAB logo.png GWAB: A web server for network-based boosting of human genome-wide association data


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


Logo morphin.png MORPHIN: Network-assisted prediction of disease pathways in model organisms


Cover title riddle.jpg RIDDLE: Network-assisted Gene Set Analysis (human only)

Co-functional Gene Networks

Laboratory Animals

MouseNetLogo.png Danionet logo.png Flynet.png WormNetv3.jpg
Mus musculus Danio rerio Drosophila melanogaster Caenorhabditis elegans

Plants

Aranet v2.jpg Maizenet logo 4th.png RiceNetv2 logo.png WheatNet logo.png Soynetlogo.png Tomatonet logo.png
Arabidopsis thaliana Zea mays Oryza sativa Triticum aestivum Glycine max Solanum lycopersicum

Fungi

Tools YesatNetLogo.jpg CryptoNet.png
Saccharomyces cerevisiae Cryptococcus neoformans

Bacteria

Pseudomonas logo.jpg Staphnet logo.JPG KlebNet logo.png EcoliNet.png XooNet logo.png
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

Jiffynetlogo4 small.jpg JiffyNet: Instant gene network building server for newly sequenced species



Network-augmented GWAS Analysis for Arabidopsis

AraGWAB logo.png 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

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