Difference between revisions of "Software"

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__NOTOC__
 
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=='''Co-functional networks and hypothesis generation servers'''==
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=='''Network Medicine Tools '''==
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[[File:TRRUST_logo.jpg |150px|link=http://www.grnpedia.org/trrust/]] '''TRRUST''': A reference database of TF-target interactions in human and mouse
  
==''Human and Animals''==
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{|border="0"  width="800"
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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: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)
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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
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[[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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==''Human and Laboratory Animals''==
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{|border="0"  width="500"
 
|align="center"|[[file:Tools_HumanNetLogo.jpg|150px|link=http://www.functionalnet.org/humannet]]
 
|align="center"|[[file:Tools_HumanNetLogo.jpg|150px|link=http://www.functionalnet.org/humannet]]
 
|align="center"|[[file:MouseNetLogo.png|150px|link=http://www.inetbio.org/mousenet]]
 
|align="center"|[[file:MouseNetLogo.png|150px|link=http://www.inetbio.org/mousenet]]
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==''Plants''==
 
==''Plants''==
{|border="0"  width="500"
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{|border="0"  width="400"
 
|align="center"|[[File:Aranet_v2.jpg|150px|link=http://www.inetbio.org/aranet]]
 
|align="center"|[[File:Aranet_v2.jpg|150px|link=http://www.inetbio.org/aranet]]
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|align="center"|[[File:Maizenet_logo_4th.png|150px|link=http://www.inetbio.org/maizenet]]
 
|align="center"|[[file:RiceNetv2 logo.png|150px|link=http://www.inetbio.org/ricenet]]
 
|align="center"|[[file:RiceNetv2 logo.png|150px|link=http://www.inetbio.org/ricenet]]
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|align="center"|[[File:WheatNet_logo.png|150px|link=http://www.inetbio.org/wheatnet]]
 
|align="center"|[[File:Soynetlogo.png|150px|link=http://www.inetbio.org/soynet]]
 
|align="center"|[[File:Soynetlogo.png|150px|link=http://www.inetbio.org/soynet]]
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|align="center"|[[File:Tomatonet_logo.png|150px|link=http://www.inetbio.org/tomatonet]]
 
|-
 
|-
 
|align="center"|''Arabidopsis thaliana''
 
|align="center"|''Arabidopsis thaliana''
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|align="center"|''Zea mays''
 
|align="center"|''Oryza sativa''
 
|align="center"|''Oryza sativa''
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|align="center"|''Triticum aestivum''
 
|align="center"|''Glycine max''
 
|align="center"|''Glycine max''
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|align="center"|''Solanum lycopersicum''
 
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|}
  
 
==''Fungi''==
 
==''Fungi''==
{|border="0"  width="400"
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{|border="0"  width="200"
 
|align="center"|[[File:Tools_YesatNetLogo.jpg|150px|link=http://www.inetbio.org/yeastnet]]
 
|align="center"|[[File:Tools_YesatNetLogo.jpg|150px|link=http://www.inetbio.org/yeastnet]]
 
|align="center"|[[file:CryptoNet.png|150px|link=http://www.inetbio.org/cryptonet]]
 
|align="center"|[[file:CryptoNet.png|150px|link=http://www.inetbio.org/cryptonet]]
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==''Bacteria''==
 
==''Bacteria''==
{|border="0"  width="400"
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{|border="0"  width="200"
 
|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]]
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|align="center"|[[File:XooNet_logo.png|150px|link=http://www.inetbio.org/xoonet]]
 
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|align="center"|''Pseudomonas aeruginosa''
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|align="center"|''Pseudomonas aeruginosa (human pathogen)''
|align="center"|''Escherichia coli''
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|align="center"|Methicillin-resistant ''Staphylococcus aureus (human pathogen)''
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|align="center"|''Klebsiella pneumoniae (human pathogen)''
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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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==''Build your own co-functional networks''==
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[[File:Jiffynetlogo4 small.jpg |150px|link=http://www.jiffynet.org]]
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'''JiffyNet''': Instant gene network building server for newly sequenced species
  
=='''Build your co-functional networks for all other species'''==
 
[[File:Jiffynetlogo4 small.jpg |150px|link=http://www.jiffynet.org]] '''JiffyNet:Instant gene network building server for newly sequenced species'''
 
  
  
  
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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''
  
  
  
=='''Network-based servers for Disease Research'''==
 
[[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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=='''Domain-based PPI networks by Weighted Mutual Information (WMI) '''==
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[[WMI|<big>'''Project Page'''</big>]]
  
  
[[File:Cover title muffinn.png |150px|link=http://www.inetbio.org/muffinn/]] '''MUFFINN (MUtations For Functional Impact on Network Neighbors): cancer gene discovery via network analysis of somatic mutation data'''
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=='''Domain2Pathway by Pathway Specificity (PS) '''==
 
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[[PS|<big>'''Project Page'''</big>]]
 
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[[File:Logo morphin.png|150px|link=http://www.inetbio.org/morphin/]] '''MORPHIN (Model Organisms Projected on a Human Integrated Gene Network): Network-assisted prediction of disease pathways in model organisms'''
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=='''Other Network Biology tools'''==
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[[File:TRRUST_logo.jpg |150px|link=http://www.grnpedia.org/trrust/]] '''TRRUST (Transcriptional Regulatory relationships Unraveled by Sentence-based Text mining): A reference database of human TF-target interactions'''
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[[File:Cover title riddle.jpg|150px|link=http://www.functionalnet.org/riddle]] '''RIDDLE (Reflective diffusion and local extension): Network-assisted Gene Set Analysis (human only)'''
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=='''Domain-based PPI networks by Weighted Mutual Information (WMI) '''==
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[[WMI|<big>'''Project Page'''</big>]]
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Revision as of 14:57, 23 February 2018

Network Medicine Tools

TRRUST logo.jpg TRRUST: A reference database of TF-target interactions 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

Human and Laboratory Animals

Tools HumanNetLogo.jpg MouseNetLogo.png Danionet logo.png Flynet.png WormNetv3.jpg
Homo sapiens 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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