Difference between revisions of "Software"
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| − | =='''CODE and DATABASE in | + | =='''CODE and DATABASE in Central Repositories'''== |
*[https://github.com/netbiolab Netbiolab GitHub site] | *[https://github.com/netbiolab Netbiolab GitHub site] | ||
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[[File:Hrgm logo.png|150px|link=//www.decodebiome.org/HRGM]] | [[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 | '''HRGM''': A Human Reference Gut Microbiome comprising 232,098 genomes for 5414 prokaryotic species and 103 million unique proteins | ||
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| + | [[File:HROM_logo.png|150px|link=//www.decodebiome.org/HROM]] | ||
| + | '''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]] | [[File:mrgm_logo.png|150px|link=//www.decodebiome.org/MRGM]] | ||
Latest revision as of 01:03, 3 November 2025
[edit] CODE and DATABASE in Central Repositories
[edit] Microbiome Research
HRGM: A Human Reference Gut Microbiome comprising 232,098 genomes for 5414 prokaryotic species and 103 million unique proteins
HROM: A Human Reference Oral Microbiome comprising 72,641 genomes for 3,426 prokaryotic species and 8.49 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)
