Difference between revisions of "Software"

From Bioinformatics Lab
Jump to: navigation, search
 
(64 intermediate revisions by 10 users not shown)
Line 1: Line 1:
 
__NOTOC__
 
__NOTOC__
=='''Co-functional networks and hypothesis generation servers'''==
+
=='''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
  
==''Human and Animal models''==
+
[[File:mrgm_logo.png|150px|link=//www.decodebiome.org/MRGM]]
{|border="0"  width="500"
+
'''MRGM''': A Mouse Reference Gut Microbiome comprising 46,267 genomes for 1,689 bacterial species and 15.2 million proteins
|align="center"|[[file:Tools_HumanNetLogo.jpg|150px|link=http://www.functionalnet.org/humannet]]
+
 
|align="center"|[[file:MouseNetLogo.png|150px|link=http://www.inetbio.org/mousenet]]
+
=='''Single-cell Biology'''==
|align="center"|[[file:danionet_logo.png|150px|link=http://www.inetbio.org/danionet]]
+
[[File:ScHumanNet github banner.final.jpg|150px|link=https://github.com/netbiolab/scHumanNet]]
|align="center"|[[file:Flynet.png|150px|link=http://www.inetbio.org/flynet]]
+
'''scHumanNet''': Cell-type-specific functional gene networks using single-cell RNA-sequencing data
|align="center"|[[file:WormNetv3.jpg|150px|link=http://www.inetbio.org/wormnet]]
+
 
 +
[[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"|''Homo sapiens''
 
 
|align="center"|''Mus musculus''
 
|align="center"|''Mus musculus''
 
|align="center"|''Danio rerio''
 
|align="center"|''Danio rerio''
Line 19: Line 50:
 
==''Plants''==
 
==''Plants''==
 
{|border="0"  width="400"
 
{|border="0"  width="400"
|align="center"|[[File:Aranet_v2.jpg|150px|link=http://www.inetbio.org/aranet]]
+
|align="center"|[[File:Aranet_v2.jpg|150px|link=//www.inetbio.org/aranet]]
|align="center"|[[File:Maizenet_logo_4th.png|150px|link=http://www.inetbio.org/maizenet]]
+
|align="center"|[[File:Maizenet_logo_4th.png|150px|link=//www.inetbio.org/maizenet]]
|align="center"|[[file:RiceNetv2 logo.png|150px|link=http://www.inetbio.org/ricenet]]
+
|align="center"|[[file:RiceNetv2 logo.png|150px|link=//www.inetbio.org/ricenet]]
|align="center"|[[File:Soynetlogo.png|150px|link=http://www.inetbio.org/soynet]]
+
|align="center"|[[File:WheatNet_logo.png|150px|link=//www.inetbio.org/wheatnet]]
|align="center"|[[File:Tomatonet_logo.png|150px|link=http://www.inetbio.org/tomatonet]]
+
|align="center"|[[File:BarleyNet_logo.png|150px|link=//www.inetbio.org/barleynet]]
|align="center"|[[File:WheatNet_logo.png|150px|link=http://www.inetbio.org/wheatnet]]
+
|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"|''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''
 
|align="center"|''Solanum lycopersicum''
|align="center"|''Triticum aestivum''
 
 
|}
 
|}
  
 
==''Fungi''==
 
==''Fungi''==
 
{|border="0"  width="200"
 
{|border="0"  width="200"
|align="center"|[[File:Tools_YesatNetLogo.jpg|150px|link=http://www.inetbio.org/yeastnet]]
+
|align="center"|[[File:Tools_YesatNetLogo.jpg|150px|link=//www.inetbio.org/yeastnet]]
|align="center"|[[file:CryptoNet.png|150px|link=http://www.inetbio.org/cryptonet]]
+
|align="center"|[[file:CryptoNet.png|150px|link=//www.inetbio.org/cryptonet]]
 
|-
 
|-
 
|align="center"|''Saccharomyces cerevisiae''
 
|align="center"|''Saccharomyces cerevisiae''
Line 45: Line 78:
 
==''Bacteria''==
 
==''Bacteria''==
 
{|border="0"  width="200"
 
{|border="0"  width="200"
|align="center"|[[File:Pseudomonas logo.jpg|150px|link=http://www.inetbio.org/pseudomonasnet]]
+
|align="center"|[[File:Pseudomonas logo.jpg|150px|link=//www.inetbio.org/pseudomonasnet]]
|align="center"|[[File:EcoliNet.png|150px|link=http://www.inetbio.org/ecolinet]]
+
|align="center"|[[File:Staphnet_logo.JPG|150px|link=//www.inetbio.org/staphnet]]
|align="center"|[[File:XooNet_logo.png|150px|link=http://www.inetbio.org/xoonet]]
+
|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''
+
|align="center"|''Pseudomonas aeruginosa (human pathogen)''
|align="center"|''Escherichia coli''
+
|align="center"|Methicillin-resistant ''Staphylococcus aureus (human pathogen)''
|align="center"|''Xanthomonas oryzae pv. oryzae''
+
|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
  
  
=='''Build your co-functional networks for all other species'''==
+
=='''Network-augmented GWAS Analysis for Arabidopsis'''==
[[File:Jiffynetlogo4 small.jpg |150px|link=http://www.jiffynet.org]]
+
[[File:araGWAB_logo.png|150px|link=//www.inetbio.org/aragwab]]
'''JiffyNet''': Instant gene network building server for newly sequenced species
+
'''araGWAB''': genome-wide association boosting for ''Arabidopsis thaliana''
  
  
 +
=='''Domain-based PPI networks by Weighted Mutual Information (WMI) '''==
 +
[[WMI|<big>'''Project Page'''</big>]]
  
  
=='''Network-based servers for Disease Research'''==
+
=='''Domain2Pathway by Pathway Specificity (PS) '''==
[[File:Coexpedia.png |150px|link=http://www.coexpedia.org]] '''COEXPEDIA''': Exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH)
+
[[PS|<big>'''Project Page'''</big>]]
 
+
 
+
[[File:GWAB_logo.png |150px|link=http://www.inetbio.org/gwab]] '''GWAB''': A web server for network-based boosting of human genome-wide association data
+
 
+
 
+
[[File:Cover title muffinn.png |150px|link=http://www.inetbio.org/muffinn/]] '''MUFFINN''': Cancer gene discovery via network analysis of somatic mutation data
+
 
+
 
+
 
+
[[File:Logo morphin.png|150px|link=http://www.inetbio.org/morphin/]] '''MORPHIN''': Network-assisted prediction of disease pathways in model organisms
+
 
+
 
+
 
+
 
+
 
+
 
+
=='''Other Network Biology tools'''==
+
[[File:TRRUST_logo.jpg |150px|link=http://www.grnpedia.org/trrust/]] '''TRRUST''': A reference database of human TF-target interactions
+
 
+
 
+
 
+
[[File:Cover title riddle.jpg|150px|link=http://www.functionalnet.org/riddle]] '''RIDDLE''': Network-assisted Gene Set Analysis (human only)
+
 
+
 
+
 
+
 
+
 
+
 
+
=='''Domain-based PPI networks by Weighted Mutual Information (WMI) '''==
+
[[WMI|<big>'''Project Page'''</big>]]
+

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

Personal tools
Namespaces

Variants
Actions
Navigation
Toolbox