Difference between revisions of "Software"

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__NOTOC__
__NOTOC__
=='''Co-functional networks: Organism-specific network-assisted hypothesis generation servers'''==
=='''CODE and DATABASE in Central Repositories'''==
*[https://github.com/netbiolab Netbiolab GitHub site]
*[https://huggingface.co/netbiolab Netbiolab HuggingFace site]


==''Animal''==
=='''Microbiome Research'''==
{|border="0"  width="800"
[[File:Hrgm logo.png|150px|link=//www.decodebiome.org/HRGM]]
|align="center"|[[file:Tools_HumanNetLogo.jpg|150px|link=http://www.functionalnet.org/humannet]]
'''HRGM''': A Human Reference Gut Microbiome comprising 232,098 genomes for 5414 prokaryotic species and 103 million unique proteins
|align="center"|[[file:MouseNetLogo.png|150px|link=http://www.inetbio.org/mousenet]]
 
|align="center"|[[file:danionet_logo.png|150px|link=http://www.inetbio.org/danionet]]
 
|align="center"|[[file:Flynet.png|150px|link=http://www.inetbio.org/flynet]]
[[File:HROM_logo.png|150px|link=//www.decodebiome.org/HROM]]
|align="center"|[[file:WormNetv3.jpg|150px|link=http://www.inetbio.org/wormnet]]
'''HROM''': A Human Reference Oral Microbiome comprising 72,641 genomes for 3,426 prokaryotic species and 8.49 million unique proteins
 
[[File:mrgm_logo.png|150px|link=//www.decodebiome.org/MRGM]]
'''MRGM''': A Mouse Reference Gut Microbiome comprising 46,267 genomes for 1,689 bacterial species and 15.2 million proteins
 
[[File:Mrgv_logo_ad.png|150px|link=//www.decodebiome.org/MRGV]]
'''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'''==
[[File:ScHumanNet github banner.final.jpg|150px|link=https://github.com/netbiolab/scHumanNet]]
'''scHumanNet''': Cell-type-specific functional gene networks using single-cell RNA-sequencing data
 
[[File:VC_logo.png|150px|link=//www.grnpedia.org/cytometry]]
'''VirtualCytometry''': A webserver for the study of immune cell differentiation using single-cell RNA sequencing data.''
 
 
=='''Network Medicine'''==
[[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=//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:Ngsea logo1.png |150px|link=//www.inetbio.org/ngsea/]] '''NGSEA''': Network-augmented gene set enrichment analysis tool
 
[[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=//www.inetbio.org/gwab]] '''GWAB''': A web server for network-based boosting of human genome-wide association data
 
[[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)
 
 
=='''Functional Gene Networks'''==
 
==''Animals''==
{|border="0"  width="400"
|align="center"|[[file:MouseNetLogo.png|150px|link=//www.inetbio.org/mousenet]]
|align="center"|[[file:danionet_logo.png|150px|link=//www.inetbio.org/danionet]]
|align="center"|[[file:Flynet.png|150px|link=//www.inetbio.org/flynet]]
|align="center"|[[file:WormNetv3.jpg|150px|link=//www.inetbio.org/wormnet]]
|-
|-
|align="center"|''Homo sapiens''
|align="center"|''Mus musculus''
|align="center"|''Mus musculus''
|align="center"|''Danio rerio''
|align="center"|''Danio rerio''
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|}
|}


==''Plant''==
==''Plants''==
{|border="0"  width="600"
{|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:RiceNetv2 logo.png|150px|link=http://www.inetbio.org/ricenet]]
|align="center"|[[File:Maizenet_logo_4th.png|150px|link=//www.inetbio.org/maizenet]]
|align="center"|[[File:Soynetlogo.png|150px|link=http://www.inetbio.org/soynet]]
|align="center"|[[file:RiceNetv2 logo.png|150px|link=//www.inetbio.org/ricenet]]
|align="center"|[[File:WheatNet_logo.png|150px|link=//www.inetbio.org/wheatnet]]
|align="center"|[[File:BarleyNet_logo.png|150px|link=//www.inetbio.org/barleynet]]
|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''
|align="center"|''Zea mays''
|align="center"|''Oryza sativa''
|align="center"|''Oryza sativa''
|align="center"|''Triticum aestivum''
|align="center"|''Hordeum vulgare''
|align="center"|''Glycine max''
|align="center"|''Glycine max''
|align="center"|''Solanum lycopersicum''
|}
|}


==''Microbe''==
==''Fungi''==
{|border="0"  width="800"
{|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"|[[File:Pseudomonas logo.jpg|150px|link=http://www.inetbio.org/pseudomonasnet]]
|align="center"|[[File:EcoliNet.png|150px|link=http://www.inetbio.org/ecolinet]]
|-
|-
|align="center"|''Saccharomyces cerevisiae''
|align="center"|''Saccharomyces cerevisiae''
|align="center"|''Cryptococcus neoformans''
|align="center"|''Cryptococcus neoformans''
|align="center"|''Pseudomonas aeruginosa''
|align="center"|''Escherichia coli''
|}
|}


==''Bacteria''==
{|border="0"  width="200"
|align="center"|[[File:Pseudomonas logo.jpg|150px|link=//www.inetbio.org/pseudomonasnet]]
|align="center"|[[File:Staphnet_logo.JPG|150px|link=//www.inetbio.org/staphnet]]
|align="center"|[[File:KlebNet_logo.png|150px|link=//www.inetbio.org/klebnet]]
|align="center"|[[File:EcoliNet.png|150px|link=//www.inetbio.org/ecolinet]]
|align="center"|[[File:XooNet_logo.png|150px|link=//www.inetbio.org/xoonet]]
|-
|align="center"|''Pseudomonas aeruginosa (human pathogen)''
|align="center"|Methicillin-resistant ''Staphylococcus aureus (human pathogen)''
|align="center"|''Klebsiella pneumoniae (human pathogen)''
|align="center"|''Escherichia coli (popular lab/factory bacterial species)''
|align="center"|''Xanthomonas oryzae pv. oryzae (rice pathogen)''
|}


=='''TRRUST: A reference database of human TF-target interactions'''==
[[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.


==''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


=='''MUFFINN: cancer gene discovery via network analysis of somatic mutation data'''==
[[File:Cover title muffinn.png |150px|link=http://www.inetbio.org/muffinn/]] MUFFINN (MUtations For Functional Impact on Network Neighbors).


=='''Network-augmented GWAS Analysis for Arabidopsis'''==
[[File:araGWAB_logo.png|150px|link=//www.inetbio.org/aragwab]]
'''araGWAB''': genome-wide association boosting for ''Arabidopsis thaliana''


=='''MORPHIN: Network-assisted prediction of disease pathways in model organisms'''==
[[File:Logo morphin.png|150px|link=http://www.inetbio.org/morphin/]] Morphin (Model Organisms Projected on a Human Integrated Gene Network) is currently available.


 
=='''Domain-based PPI networks by Weighted Mutual Information (WMI) '''==
=='''JiffyNet:Instant gene network building server for newly sequenced species'''==
[[WMI|<big>'''Project Page'''</big>]]
[[File:Jiffynetlogo4 small.jpg |150px|link=http://www.jiffynet.org]] Jiffy (instant) gene network modeler for newly sequenced species
 
 
=='''RIDDLE: Network-assisted Gene Set Analysis (human only)'''==
[[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.




=='''Domain-based PPI networks by Weighted Mutual Information (WMI) '''==
=='''Domain2Pathway by Pathway Specificity (PS) '''==
[[WMI|<big>'''Project Page'''</big>]]
[[PS|<big>'''Project Page'''</big>]]

Latest revision as of 13:38, 24 February 2026

CODE and DATABASE in Central Repositories

Microbiome Research

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


HROM logo.png HROM: A Human Reference Oral Microbiome comprising 72,641 genomes for 3,426 prokaryotic species and 8.49 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

Mrgv logo ad.png 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

Error creating thumbnail: File missing

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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