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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=='''CODE and DATABASE in Central Repositories'''==
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==''Human and Animal models''==
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*[https://github.com/netbiolab Netbiolab GitHub site]
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{|border="0"  width="800"
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*[https://huggingface.co/netbiolab Netbiolab HuggingFace site]
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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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=='''Microbiome Research'''==
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|align="center"|[[file:danionet_logo.png|150px|link=http://www.inetbio.org/danionet]]
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[[File:Hrgm logo.png|150px|link=//www.decodebiome.org/HRGM]]
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|align="center"|[[file:Flynet.png|150px|link=http://www.inetbio.org/flynet]]
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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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|align="center"|[[file:WormNetv3.jpg|150px|link=http://www.inetbio.org/wormnet]]
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[[File:HROM_logo.png|150px|link=//www.decodebiome.org/HROM]]
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'''HROM''': A Human Reference Oral Microbiome comprising 72,641 genomes for 3,426 prokaryotic species and 8.49 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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[[File:Mrgv_logo_ad.png|150px|link=//www.decodebiome.org/MRGV]]
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'''MRGV''': A Mouse Reference Gut Virome comprising 109,778 genomes for 28,824 species-level vOTUs and 1.3 million unique 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'''==
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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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 +
 
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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]]
 
|-
 
|-
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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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|}
 
|}
  
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==''Reference plant and Crops''==
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==''Plants''==
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{|border="0"  width="600"
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{|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:Soynetlogo.png|150px|link=http://www.inetbio.org/soynet]]
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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''
 
|align="center"|''Glycine max''
 
|align="center"|''Glycine max''
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|align="center"|''Solanum lycopersicum''
 
|}
 
|}
  
 
==''Fungi''==
 
==''Fungi''==
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{|border="0"  width="800"
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{|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''==
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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:Pseudomonas logo.jpg|150px|link=//www.inetbio.org/pseudomonasnet]]
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|align="center"|[[File:EcoliNet.png|150px|link=http://www.inetbio.org/ecolinet]]
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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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|align="center"|''Pseudomonas aeruginosa''
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|align="center"|''Pseudomonas aeruginosa (human pathogen)''
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|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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=='''TRRUST: A reference database of human TF-target interactions'''==
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==''Build your own Functional gene networks''==
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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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[[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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=='''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''
  
  
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=='''MUFFINN: cancer gene discovery via network analysis of somatic mutation data'''==
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=='''Domain-based PPI networks by Weighted Mutual Information (WMI) '''==
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[[File:Cover title muffinn.png |150px|link=http://www.inetbio.org/muffinn/]] MUFFINN (MUtations For Functional Impact on Network Neighbors).
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[[WMI|<big>'''Project Page'''</big>]]
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=='''MORPHIN: Network-assisted prediction of disease pathways in model organisms'''==
 
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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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=='''JiffyNet:Instant gene network building server for newly sequenced species'''==
 
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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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=='''Domain2Pathway by Pathway Specificity (PS) '''==
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[[PS|<big>'''Project Page'''</big>]]
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=='''RIDDLE: Network-assisted Gene Set Analysis (human only)'''==
 
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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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=='''Domain-based PPI networks by Weighted Mutual Information (WMI) '''==
 
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[[WMI|<big>'''Project Page'''</big>]]
 

Latest revision as of 13:38, 24 February 2026

CODE and DATABASE in Central Repositories

Microbiome Research

150px HRGM: A Human Reference Gut Microbiome comprising 232,098 genomes for 5414 prokaryotic species and 103 million unique proteins


150px HROM: A Human Reference Oral Microbiome comprising 72,641 genomes for 3,426 prokaryotic species and 8.49 million unique proteins

150px MRGM: A Mouse Reference Gut Microbiome comprising 46,267 genomes for 1,689 bacterial species and 15.2 million proteins

150px MRGV: A Mouse Reference Gut Virome comprising 109,778 genomes for 28,824 species-level vOTUs and 1.3 million unique proteins

Single-cell Biology

150px scHumanNet: Cell-type-specific functional gene networks using single-cell RNA-sequencing data

150px VirtualCytometry: A webserver for the study of immune cell differentiation using single-cell RNA sequencing data.


Network Medicine

150pxHumanNet: Human gene networks for disease research

150px TRRUST: Curated TF-target interaction networks in human and mouse

150px COEXPEDIA: Exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH)

150px NGSEA: Network-augmented gene set enrichment analysis tool

150px MUFFINN: Cancer gene discovery via network analysis of somatic mutation data

150px GWAB: A web server for network-based boosting of human genome-wide association data

150px MORPHIN: Network-assisted prediction of disease pathways in model organisms

150px RIDDLE: Network-assisted Gene Set Analysis (human only)


Functional Gene Networks

Animals

150px 150px 150px 150px
Mus musculus Danio rerio Drosophila melanogaster Caenorhabditis elegans

Plants

150px 150px 150px 150px 150px 150px 150px
Arabidopsis thaliana Zea mays Oryza sativa Triticum aestivum Hordeum vulgare Glycine max Solanum lycopersicum

Fungi

150px 150px
Saccharomyces cerevisiae Cryptococcus neoformans

Bacteria

150px 150px 150px 150px 150px
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

150px BiomeNet: A database for construction and analysis of functional interaction networks for any species with a sequenced genome


Network-augmented GWAS Analysis for Arabidopsis

150px 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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