Difference between revisions of "Software"

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__NOTOC__
 
__NOTOC__
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=='''Gene Regulation Research Tools'''==
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=='''Microbiome Research'''==
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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
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[[File:Hrgm logo.png|150px|link=//www.decodebiome.org/HRGM]]
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'''HRGM''': A Human Reference Gut Microbiome comprising 232,098 genomes for 5414 prokaryotic species and 103 million unique proteins
  
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[[File:mrgm_logo.png|150px|link=//www.decodebiome.org/MRGM]]
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'''MRGM''': A Mouse Reference Gut Microbiome comprising 46,267 genomes for 1,689 bacterial species and 15.2 million proteins
  
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=='''Single-cell Biology'''==
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[[File:ScHumanNet github banner.final.jpg|150px|link=https://github.com/netbiolab/scHumanNet]]
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'''scHumanNet''': Cell-type-specific functional gene networks using single-cell RNA-sequencing data
  
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[[File:VC_logo.png|150px|link=//www.grnpedia.org/cytometry]]
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'''VirtualCytometry''': A webserver for the study of immune cell differentiation using single-cell RNA sequencing data.''
  
  
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=='''Network Medicine Tools '''==
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=='''Network Medicine'''==
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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:HumanNet_logo_with_title.png|150px|link=//www.inetbio.org/humannet]]'''HumanNet''': Human gene networks for disease research
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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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+
  
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[[File:TRRUST_logo.jpg |150px|link=//www.grnpedia.org/trrust/]] '''TRRUST''': Curated TF-target interaction networks in human and mouse
  
 
[[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:Ngsea logo1.png |150px|link=//www.inetbio.org/ngsea/]] '''NGSEA''': Network-augmented gene set enrichment analysis tool
  
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[[File:Cover title muffinn.png |150px|link=//www.inetbio.org/muffinn/]] '''MUFFINN''': Cancer gene discovery via network analysis of somatic mutation 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
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[[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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+
  
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[[File:Logo morphin.png|150px|link=//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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=='''Functional Gene Networks'''==
  
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==''Animals''==
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{|border="0"  width="400"
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=='''Co-functional Gene Networks'''==
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|align="center"|[[file:MouseNetLogo.png|150px|link=//www.inetbio.org/mousenet]]
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|align="center"|[[file:danionet_logo.png|150px|link=//www.inetbio.org/danionet]]
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==''Human and Laboratory Animals''==
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|align="center"|[[file:Flynet.png|150px|link=//www.inetbio.org/flynet]]
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{|border="0"  width="500"
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|align="center"|[[file:WormNetv3.jpg|150px|link=//www.inetbio.org/wormnet]]
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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]]
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|align="center"|[[file:danionet_logo.png|150px|link=http://www.inetbio.org/danionet]]
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|align="center"|[[file:Flynet.png|150px|link=http://www.inetbio.org/flynet]]
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|align="center"|[[file:WormNetv3.jpg|150px|link=http://www.inetbio.org/wormnet]]
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|-
 
|-
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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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==''Plants''==
 
==''Plants''==
 
{|border="0"  width="400"
 
{|border="0"  width="400"
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|align="center"|[[File:Aranet_v2.jpg|150px|link=http://www.inetbio.org/aranet]]
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|align="center"|[[File:Aranet_v2.jpg|150px|link=//www.inetbio.org/aranet]]
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|align="center"|[[File:Maizenet_logo_4th.png|150px|link=http://www.inetbio.org/maizenet]]
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|align="center"|[[File:Maizenet_logo_4th.png|150px|link=//www.inetbio.org/maizenet]]
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|align="center"|[[file:RiceNetv2 logo.png|150px|link=http://www.inetbio.org/ricenet]]
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|align="center"|[[file:RiceNetv2 logo.png|150px|link=//www.inetbio.org/ricenet]]
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|align="center"|[[File:WheatNet_logo.png|150px|link=http://www.inetbio.org/wheatnet]]
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|align="center"|[[File:WheatNet_logo.png|150px|link=//www.inetbio.org/wheatnet]]
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|align="center"|[[File:Soynetlogo.png|150px|link=http://www.inetbio.org/soynet]]
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|align="center"|[[File:BarleyNet_logo.png|150px|link=//www.inetbio.org/barleynet]]
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|align="center"|[[File:Tomatonet_logo.png|150px|link=http://www.inetbio.org/tomatonet]]
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|align="center"|[[File:Soynetlogo.png|150px|link=//www.inetbio.org/soynet]]
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|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''
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|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"
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|align="center"|[[File:Tools_YesatNetLogo.jpg|150px|link=http://www.inetbio.org/yeastnet]]
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|align="center"|[[File:Tools_YesatNetLogo.jpg|150px|link=//www.inetbio.org/yeastnet]]
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|align="center"|[[file:CryptoNet.png|150px|link=http://www.inetbio.org/cryptonet]]
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|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"
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|align="center"|[[File:Pseudomonas logo.jpg|150px|link=http://www.inetbio.org/pseudomonasnet]]
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|align="center"|[[File:Pseudomonas logo.jpg|150px|link=//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:Staphnet_logo.JPG|150px|link=//www.inetbio.org/staphnet]]
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|align="center"|[[File:KlebNet_logo.png|150px|link=http://www.inetbio.org/klebnet]]
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|align="center"|[[File:KlebNet_logo.png|150px|link=//www.inetbio.org/klebnet]]
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|align="center"|[[File:EcoliNet.png|150px|link=http://www.inetbio.org/ecolinet]]
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|align="center"|[[File:EcoliNet.png|150px|link=//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"|[[File:XooNet_logo.png|150px|link=//www.inetbio.org/xoonet]]
 
|-
 
|-
 
|align="center"|''Pseudomonas aeruginosa (human pathogen)''
 
|align="center"|''Pseudomonas aeruginosa (human pathogen)''
 
|align="center"|Methicillin-resistant ''Staphylococcus aureus (human pathogen)''
 
|align="center"|Methicillin-resistant ''Staphylococcus aureus (human pathogen)''
 
|align="center"|''Klebsiella pneumoniae (human pathogen)''
 
|align="center"|''Klebsiella pneumoniae (human pathogen)''
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|align="center"|''Escherichia coli (laboratory strain)''
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|align="center"|''Escherichia coli (popular lab/factory bacterial species)''
 
|align="center"|''Xanthomonas oryzae pv. oryzae (rice pathogen)''
 
|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
 
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==''Build your own Functional gene networks''==
 +
[[File:BiomeNet_logo.png | 150px | link=http://kobic.re.kr/biomenet]]
 +
'''BiomeNet''': A database for construction and analysis of functional interaction networks for any species with a sequenced genome
  
  
 +
=='''Network-augmented GWAS Analysis for Arabidopsis'''==
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[[File:araGWAB_logo.png|150px|link=//www.inetbio.org/aragwab]]
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'''araGWAB''': genome-wide association boosting for ''Arabidopsis thaliana''
  
  

Revision as of 17:00, 6 March 2024

Microbiome Research

Hrgm logo.png HRGM: A Human Reference Gut Microbiome comprising 232,098 genomes for 5414 prokaryotic species and 103 million unique proteins

Mrgm logo.png MRGM: A Mouse Reference Gut Microbiome comprising 46,267 genomes for 1,689 bacterial species and 15.2 million proteins

Single-cell Biology

ScHumanNet github banner.final.jpg scHumanNet: Cell-type-specific functional gene networks using single-cell RNA-sequencing data

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


Network Medicine

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

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

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

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

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)


Functional Gene Networks

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 Functional gene 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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