Difference between revisions of "Software"

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__NOTOC__
 
__NOTOC__
 
=='''Single-cell Omics Data Analysis Tools'''==
 
=='''Single-cell Omics Data Analysis Tools'''==
−
[[File:VC_logo.png|200px|link=http://www.grnpedia.org/cytometry]]
+
[[File:VC_logo.png|200px|link=//www.grnpedia.org/cytometry]]
 
'''VirtualCytometry''': A webserver for the study of immune cell differentiation using single-cell RNA sequencing data.''
 
'''VirtualCytometry''': A webserver for the study of immune cell differentiation using single-cell RNA sequencing data.''
  
  
 
=='''Network Medicine Tools '''==
 
=='''Network Medicine Tools '''==
−
[[File:HumanNet_logo_with_title.png|150px|link=http://www.inetbio.org/humannet]]'''HumanNet''': Human gene networks for disease research
+
[[File:HumanNet_logo_with_title.png|150px|link=//www.inetbio.org/humannet]]'''HumanNet''': Human gene networks for disease research
  
  
−
[[File:TRRUST_logo.jpg |150px|link=http://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
  
  
−
[[File:Ngsea logo1.png |150px|link=https://www.inetbio.org/ngsea/]] '''NGSEA''': Network-augmented gene set enrichment analysis tool
+
[[File:Ngsea logo1.png |150px|link=//www.inetbio.org/ngsea/]] '''NGSEA''': Network-augmented gene set enrichment analysis tool
  
  
−
[[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=//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=//www.inetbio.org/gwab]] '''GWAB''': A web server for network-based boosting of human genome-wide association data
  
  
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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=//www.inetbio.org/morphin/]] '''MORPHIN''': Network-assisted prediction of disease pathways in model organisms
  
  
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==''Laboratory Animals''==
 
==''Laboratory Animals''==
 
{|border="0"  width="400"
 
{|border="0"  width="400"
−
|align="center"|[[file:MouseNetLogo.png|150px|link=http://www.inetbio.org/mousenet]]
+
|align="center"|[[file:MouseNetLogo.png|150px|link=//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=//www.inetbio.org/danionet]]
−
|align="center"|[[file:Flynet.png|150px|link=http://www.inetbio.org/flynet]]
+
|align="center"|[[file:Flynet.png|150px|link=//www.inetbio.org/flynet]]
−
|align="center"|[[file:WormNetv3.jpg|150px|link=http://www.inetbio.org/wormnet]]
+
|align="center"|[[file:WormNetv3.jpg|150px|link=//www.inetbio.org/wormnet]]
 
|-
 
|-
 
|align="center"|''Mus musculus''
 
|align="center"|''Mus musculus''
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==''Plants''==
 
==''Plants''==
 
{|border="0"  width="400"
 
{|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=//www.inetbio.org/aranet]]
−
|align="center"|[[File:Maizenet_logo_4th.png|150px|link=http://www.inetbio.org/maizenet]]
+
|align="center"|[[File:Maizenet_logo_4th.png|150px|link=//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=//www.inetbio.org/ricenet]]
−
|align="center"|[[File:WheatNet_logo.png|150px|link=http://www.inetbio.org/wheatnet]]
+
|align="center"|[[File:WheatNet_logo.png|150px|link=//www.inetbio.org/wheatnet]]
−
|align="center"|[[File:Soynetlogo.png|150px|link=http://www.inetbio.org/soynet]]
+
|align="center"|[[File:BarleyNet_logo.png|150px|link=//www.inetbio.org/barleynet]]
−
|align="center"|[[File:Tomatonet_logo.png|150px|link=http://www.inetbio.org/tomatonet]]
+
|align="center"|[[File:Soynetlogo.png|150px|link=//www.inetbio.org/soynet]]
 +
|align="center"|[[File:Tomatonet_logo.png|150px|link=//www.inetbio.org/tomatonet]]
 
|-
 
|-
 
|align="center"|''Arabidopsis thaliana''
 
|align="center"|''Arabidopsis thaliana''
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|align="center"|''Oryza sativa''
 
|align="center"|''Oryza sativa''
 
|align="center"|''Triticum aestivum''
 
|align="center"|''Triticum aestivum''
 +
|align="center"|''Hordeum vulgare''
 
|align="center"|''Glycine max''
 
|align="center"|''Glycine max''
 
|align="center"|''Solanum lycopersicum''
 
|align="center"|''Solanum lycopersicum''
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==''Fungi''==
 
==''Fungi''==
 
{|border="0"  width="200"
 
{|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=//www.inetbio.org/yeastnet]]
−
|align="center"|[[file:CryptoNet.png|150px|link=http://www.inetbio.org/cryptonet]]
+
|align="center"|[[file:CryptoNet.png|150px|link=//www.inetbio.org/cryptonet]]
 
|-
 
|-
 
|align="center"|''Saccharomyces cerevisiae''
 
|align="center"|''Saccharomyces cerevisiae''
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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:Pseudomonas logo.jpg|150px|link=//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=//www.inetbio.org/staphnet]]
−
|align="center"|[[File:KlebNet_logo.png|150px|link=http://www.inetbio.org/klebnet]]
+
|align="center"|[[File:KlebNet_logo.png|150px|link=//www.inetbio.org/klebnet]]
−
|align="center"|[[File:EcoliNet.png|150px|link=http://www.inetbio.org/ecolinet]]
+
|align="center"|[[File:EcoliNet.png|150px|link=//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=//www.inetbio.org/xoonet]]
 
|-
 
|-
 
|align="center"|''Pseudomonas aeruginosa (human pathogen)''
 
|align="center"|''Pseudomonas aeruginosa (human pathogen)''
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=='''Network-augmented GWAS Analysis for Arabidopsis'''==
 
=='''Network-augmented GWAS Analysis for Arabidopsis'''==
−
[[File:araGWAB_logo.png|150px|link=http://www.inetbio.org/aragwab]]
+
[[File:araGWAB_logo.png|150px|link=//www.inetbio.org/aragwab]]
 
'''araGWAB''': genome-wide association boosting for ''Arabidopsis thaliana''
 
'''araGWAB''': genome-wide association boosting for ''Arabidopsis thaliana''
  

Revision as of 14:53, 17 October 2019

Single-cell Omics Data Analysis Tools

VC logo.png VirtualCytometry: A webserver for the study of immune cell differentiation using single-cell RNA sequencing data.


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


Ngsea logo1.png NGSEA: Network-augmented gene set enrichment analysis tool


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 BarleyNet logo.png Soynetlogo.png Tomatonet logo.png
Arabidopsis thaliana Zea mays Oryza sativa Triticum aestivum Hordeum vulgare 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

BiomeNet logo.png 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 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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