Difference between revisions of "Software"
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− | ==''' | + | =='''Microbiome Research'''== |
+ | [[File:Hrgm logo.png|150px|link=//www.decodebiome.org/HRGM]] | ||
+ | '''HRGM''': A Human Reference Gut Microbiome comprising 232,098 genomes for 5414 prokaryotic species and 103 million unique proteins | ||
− | =='' | + | [[File:mrgm_logo.png|150px|link=//www.decodebiome.org/MRGM]] |
− | {|border="0" width=" | + | '''MRGM''': A Mouse Reference Gut Microbiome comprising 46,267 genomes for 1,689 bacterial species and 15.2 million proteins |
− | |align="center"|[[file: | + | |
− | |align="center"|[[file: | + | =='''Single-cell Biology'''== |
− | |align="center"|[[file: | + | [[File:ScHumanNet github banner.final.jpg|150px|link=https://github.com/netbiolab/scHumanNet]] |
− | |align="center"|[[file: | + | '''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"|''Mus musculus'' | |align="center"|''Mus musculus'' | ||
− | |align="center"|'' | + | |align="center"|''Danio rerio'' |
|align="center"|''Drosophila melanogaster'' | |align="center"|''Drosophila melanogaster'' | ||
+ | |align="center"|''Caenorhabditis elegans'' | ||
|} | |} | ||
− | =='' | + | ==''Plants''== |
{|border="0" width="400" | {|border="0" width="400" | ||
− | |align="center"|[[File:Aranet_v2.jpg|150px|link= | + | |align="center"|[[File:Aranet_v2.jpg|150px|link=//www.inetbio.org/aranet]] |
− | |align="center"|[[file:RiceNetv2 logo.png|150px|link= | + | |align="center"|[[File:Maizenet_logo_4th.png|150px|link=//www.inetbio.org/maizenet]] |
− | |align="center"|[[File: | + | |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'' | ||
|} | |} | ||
− | =='' | + | ==''Fungi''== |
− | {|border="0" width=" | + | {|border="0" width="200" |
− | |align="center"|[[File:Tools_YesatNetLogo.jpg|150px|link= | + | |align="center"|[[File:Tools_YesatNetLogo.jpg|150px|link=//www.inetbio.org/yeastnet]] |
− | |align="center"|[[file:CryptoNet.png|150px|link= | + | |align="center"|[[file:CryptoNet.png|150px|link=//www.inetbio.org/cryptonet]] |
− | + | ||
− | + | ||
|- | |- | ||
|align="center"|''Saccharomyces cerevisiae'' | |align="center"|''Saccharomyces cerevisiae'' | ||
|align="center"|''Cryptococcus neoformans'' | |align="center"|''Cryptococcus neoformans'' | ||
− | |||
− | |||
|} | |} | ||
+ | ==''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)'' | ||
+ | |} | ||
− | |||
− | |||
+ | ==''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'''== | |
− | ==''' | + | [[File:araGWAB_logo.png|150px|link=//www.inetbio.org/aragwab]] |
− | [[File: | + | '''araGWAB''': genome-wide association boosting for ''Arabidopsis thaliana'' |
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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>]] | ||
+ | |||
+ | |||
+ | =='''Domain2Pathway by Pathway Specificity (PS) '''== | ||
+ | [[PS|<big>'''Project Page'''</big>]] |
Latest revision as of 17:00, 6 March 2024
[edit] Microbiome Research
HRGM: A Human Reference Gut Microbiome comprising 232,098 genomes for 5414 prokaryotic species and 103 million unique proteins
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: Cell-type-specific functional gene networks using single-cell RNA-sequencing data
VirtualCytometry: A webserver for the study of immune cell differentiation using single-cell RNA sequencing data.
[edit] Network Medicine
HumanNet: Human gene networks for disease research
TRRUST: Curated TF-target interaction networks in human and mouse
COEXPEDIA: Exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH)
NGSEA: Network-augmented gene set enrichment analysis tool
MUFFINN: Cancer gene discovery via network analysis of somatic mutation data
GWAB: A web server for network-based boosting of human genome-wide association data
MORPHIN: Network-assisted prediction of disease pathways in model organisms
RIDDLE: Network-assisted Gene Set Analysis (human only)
[edit] Functional Gene Networks
[edit] Animals
Mus musculus | Danio rerio | Drosophila melanogaster | Caenorhabditis elegans |
[edit] Plants
Arabidopsis thaliana | Zea mays | Oryza sativa | Triticum aestivum | Hordeum vulgare | Glycine max | Solanum lycopersicum |
[edit] Fungi
Saccharomyces cerevisiae | Cryptococcus neoformans |
[edit] Bacteria
[edit] Build your own Functional gene networks
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: genome-wide association boosting for Arabidopsis thaliana
[edit] Domain-based PPI networks by Weighted Mutual Information (WMI)