Difference between revisions of "Software"

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__NOTOC__
 
__NOTOC__
 
=='''Microbiome Research'''==
 
=='''Microbiome Research'''==
[[File:Hrgm logo.png|150px|link=//www.mbiomenet.org/HRGM]]
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[[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
  
[[File:mrgm_logo.png|150px|link=//www.mbiomenet.org/MRGM]]
+
[[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
 
'''MRGM''': A Mouse Reference Gut Microbiome comprising 46,267 genomes for 1,689 bacterial species and 15.2 million proteins
  
 
=='''Single-cell Biology'''==
 
=='''Single-cell Biology'''==
[[File:ScHumanNet github banner.final.jpg|200px|link=https://github.com/netbiolab/scHumanNet]]
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[[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
 
'''scHumanNet''': Cell-type-specific functional gene networks using single-cell RNA-sequencing data
  
[[File:VC_logo.png|200px|link=//www.grnpedia.org/cytometry]]
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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.''
  

Latest revision as of 17:00, 6 March 2024

[edit] Microbiome Research

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

[edit] Single-cell Biology

ScHumanNet github banner.final.jpg 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.


[edit] 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)


[edit] Functional Gene Networks

[edit] 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 Functional gene 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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