Difference between revisions of "Software"

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=='''Human Microbiome Data Analysis Tools'''==
 
[[File:Hrgm logo.png|200px|link=//www.mbiomenet.org/HRGM]]
 
[[File:Hrgm logo.png|200px|link=//www.mbiomenet.org/HRGM]]
 
'''HRGM''': Human reference gut microbiome of 5,414 prokaryotic species including newly assembled genomes from under-represented Asian metagenomes.
 
'''HRGM''': Human reference gut microbiome of 5,414 prokaryotic species including newly assembled genomes from under-represented Asian metagenomes.

Latest revision as of 15:37, 13 November 2020

[edit] Human Microbiome Data Analysis Tools

Hrgm logo.png HRGM: Human reference gut microbiome of 5,414 prokaryotic species including newly assembled genomes from under-represented Asian metagenomes.


[edit] Single-cell Omics Data Analysis Tools

VC logo.png VirtualCytometry: A webserver for the study of immune cell differentiation using single-cell RNA sequencing data.


[edit] Network Medicine Tools

HumanNet logo with title.pngHumanNet: Human gene networks for disease research


TRRUST logo.jpg TRRUST: Curated TF-target interaction networks in human and mouse


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


Coexpedia.png COEXPEDIA: Exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH)


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)


[edit] Co-functional Gene Networks

[edit] Laboratory Animals

MouseNetLogo.png Danionet logo.png Flynet.png WormNetv3.jpg
Mus musculus Danio rerio Drosophila melanogaster Caenorhabditis elegans

[edit] 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

[edit] Fungi

Tools YesatNetLogo.jpg CryptoNet.png
Saccharomyces cerevisiae Cryptococcus neoformans

[edit] 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)


[edit] Build your own co-functional networks

BiomeNet logo.png 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 logo.png araGWAB: genome-wide association boosting for Arabidopsis thaliana



[edit] Domain-based PPI networks by Weighted Mutual Information (WMI)

Project Page


[edit] Domain2Pathway by Pathway Specificity (PS)

Project Page

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