Difference between revisions of "Software"
From Bioinformatics Lab
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| − | ==''' | + | =='''Microbiome Research'''== |
| − | [[File:Hrgm logo.png| | + | [[File:Hrgm logo.png|150px|link=//www.decodebiome.org/HRGM]] |
| − | '''HRGM''': Human | + | '''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]] | ||
| + | '''MRGM''': A Mouse Reference Gut Microbiome comprising 46,267 genomes for 1,689 bacterial species and 15.2 million proteins | ||
| − | =='''Single-cell | + | =='''Single-cell Biology'''== |
| − | [[File:VC_logo.png| | + | [[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 | ||
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| + | [[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.'' | '''VirtualCytometry''': A webserver for the study of immune cell differentiation using single-cell RNA sequencing data.'' | ||
| − | =='''Network Medicine | + | =='''Network Medicine'''== |
[[File:HumanNet_logo_with_title.png|150px|link=//www.inetbio.org/humannet]]'''HumanNet''': Human gene networks for disease research | [[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 | [[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: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 | [[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 | [[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 | [[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) | [[File:Cover title riddle.jpg|150px|link=http://www.functionalnet.org/riddle]] '''RIDDLE''': Network-assisted Gene Set Analysis (human only) | ||
| + | =='''Functional Gene Networks'''== | ||
| − | =='' | + | ==''Animals''== |
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{|border="0" width="400" | {|border="0" width="400" | ||
|align="center"|[[file:MouseNetLogo.png|150px|link=//www.inetbio.org/mousenet]] | |align="center"|[[file:MouseNetLogo.png|150px|link=//www.inetbio.org/mousenet]] | ||
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| − | ==''Build your own | + | ==''Build your own Functional gene networks''== |
[[File:BiomeNet_logo.png | 150px | link=http://kobic.re.kr/biomenet]] | [[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 | '''BiomeNet''': A database for construction and analysis of functional interaction networks for any species with a sequenced genome | ||
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[[File:araGWAB_logo.png|150px|link=//www.inetbio.org/aragwab]] | [[File:araGWAB_logo.png|150px|link=//www.inetbio.org/aragwab]] | ||
'''araGWAB''': genome-wide association boosting for ''Arabidopsis thaliana'' | '''araGWAB''': genome-wide association boosting for ''Arabidopsis thaliana'' | ||
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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
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| Mus musculus | Danio rerio | Drosophila melanogaster | Caenorhabditis elegans |
[edit] Plants
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| Arabidopsis thaliana | Zea mays | Oryza sativa | Triticum aestivum | Hordeum vulgare | Glycine max | Solanum lycopersicum |
[edit] Fungi
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| Saccharomyces cerevisiae | Cryptococcus neoformans |
[edit] Bacteria
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| 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: 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)
