Difference between revisions of "Software"

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__NOTOC__
 
__NOTOC__
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=='''Co-functional networks: Organism-specific network-assisted hypothesis generation servers'''==
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=='''Microbiome Research'''==
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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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==''Animal''==
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[[File:mrgm_logo.png|150px|link=//www.decodebiome.org/MRGM]]
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{|border="0"  width="800"
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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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|align="center"|[[file:MouseNetLogo.png|150px|link=http://www.inetbio.org/mousenet]]
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|align="center"|[[file:WormNetv3.jpg|150px|link=http://www.inetbio.org/wormnet]]
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=='''Single-cell Biology'''==
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|align="center"|[[file:Flynet.png|150px|link=http://www.inetbio.org/flynet]]
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[[File:ScHumanNet github banner.final.jpg|150px|link=https://github.com/netbiolab/scHumanNet]]
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|align="center"|[[file:Tools_HumanNetLogo.jpg|150px|link=http://www.functionalnet.org/humannet]]
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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'''==
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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:TRRUST_logo.jpg |150px|link=//www.grnpedia.org/trrust/]] '''TRRUST''': Curated TF-target interaction networks in human and mouse
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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: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: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=//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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=='''Functional Gene Networks'''==
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==''Animals''==
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{|border="0"  width="400"
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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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|align="center"|[[file:Flynet.png|150px|link=//www.inetbio.org/flynet]]
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|align="center"|[[file:WormNetv3.jpg|150px|link=//www.inetbio.org/wormnet]]
 
|-
 
|-
 
|align="center"|''Mus musculus''
 
|align="center"|''Mus musculus''
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|align="center"|''Caenorhabditis elegans''
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|align="center"|''Danio rerio''
 
|align="center"|''Drosophila melanogaster''
 
|align="center"|''Drosophila melanogaster''
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|align="center"|''Homo sapiens''
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|align="center"|''Caenorhabditis elegans''
 
|}
 
|}
  
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==''Plant''==
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==''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:RiceNetv2 logo.png|150px|link=http://www.inetbio.org/ricenet]]
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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=//www.inetbio.org/ricenet]]
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|align="center"|[[File:WheatNet_logo.png|150px|link=//www.inetbio.org/wheatnet]]
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|align="center"|[[File:BarleyNet_logo.png|150px|link=//www.inetbio.org/barleynet]]
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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"|''Zea mays''
 
|align="center"|''Oryza sativa''
 
|align="center"|''Oryza sativa''
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|align="center"|''Triticum aestivum''
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|align="center"|''Hordeum vulgare''
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|align="center"|''Glycine max''
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|align="center"|''Solanum lycopersicum''
 
|}
 
|}
  
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==''Microbe''==
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==''Fungi''==
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{|border="0"  width="800"
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{|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:Tools_YesatNetLogo.jpg|150px|link=//www.inetbio.org/yeastnet]]
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|align="center"|[[File:EcoliNet.png|150px|link=http://www.inetbio.org/ecolinet]]
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|align="center"|[[file:CryptoNet.png|150px|link=//www.inetbio.org/cryptonet]]
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|align="center"|[[File:Tools_YesatNetLogo.jpg|150px|link=http://www.inetbio.org/yeastnet]]
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|align="center"|[[file:CryptoNet.png|150px|link=http://www.inetbio.org/cryptonet]]
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|-
 
|-
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|align="center"|''Pseudomonas aeruginosa''
 
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|align="center"|''Escherichia coli''
 
 
|align="center"|''Saccharomyces cerevisiae''
 
|align="center"|''Saccharomyces cerevisiae''
 
|align="center"|''Cryptococcus neoformans''
 
|align="center"|''Cryptococcus neoformans''
 
|}
 
|}
  
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=='''RIDDLE: Network-assisted Gene Set Analysis (human only)'''==
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==''Bacteria''==
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[[File:Cover title riddle.jpg|150px|link=http://www.functionalnet.org/riddle]] RIDDLE (Reflective diffusion and local extension) is currently available for only human genes.
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{|border="0"  width="200"
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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=//www.inetbio.org/staphnet]]
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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=//www.inetbio.org/ecolinet]]
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|align="center"|[[File:XooNet_logo.png|150px|link=//www.inetbio.org/xoonet]]
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|-
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|align="center"|''Pseudomonas aeruginosa (human pathogen)''
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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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|}
  
  
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=='''MORPHIN: Network-assisted prediction of disease pathways in model organisms'''==
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==''Build your own Functional gene networks''==
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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) is currently available.
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[[File:BiomeNet_logo.png | 150px | link=http://kobic.re.kr/biomenet]]
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'''BiomeNet''': A database for construction and analysis of functional interaction networks for any species with a sequenced genome
  
  
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=='''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:Jiffynetlogo4 small.jpg |150px|link=http://www.jiffynet.org]] Jiffy (instant) gene network modeler for newly sequenced species
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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''
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=='''TRRUST: A reference database of human TF-target interactions'''==
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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) is currently available for only human genes.
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=='''MUFFINN: a network-based method for prioritizing cancer genes'''==
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[[File:TRRUST_logo.jpg |150px|link=http://www.inetbio.org/muffinn/]] MUFFINN (MUtations For Functional Impact on Network Neighbors) is currently available.
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=='''Domain-based PPI networks by Weighted Mutual Information (WMI) '''==
 
=='''Domain-based PPI networks by Weighted Mutual Information (WMI) '''==
 
[[WMI|<big>'''Project Page'''</big>]]
 
[[WMI|<big>'''Project Page'''</big>]]
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 +
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=='''Domain2Pathway by Pathway Specificity (PS) '''==
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[[PS|<big>'''Project Page'''</big>]]

Latest revision as of 17:00, 6 March 2024

[edit] 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

[edit] 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.


[edit] 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)


[edit] Functional Gene Networks

[edit] Animals

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

[edit] 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

[edit] Fungi

Tools YesatNetLogo.jpg CryptoNet.png
Saccharomyces cerevisiae Cryptococcus neoformans

[edit] 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)


[edit] 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


[edit] Network-augmented GWAS Analysis for Arabidopsis

AraGWAB logo.png araGWAB: genome-wide association boosting for Arabidopsis thaliana


[edit] Domain-based PPI networks by Weighted Mutual Information (WMI)

Project Page


[edit] Domain2Pathway by Pathway Specificity (PS)

Project Page

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