Difference between revisions of "Software"

From Bioinformatics Lab
Jump to: navigation, search
(→‎Domain-based PPI networks by Weighted Mutual Information (WMI))
 
(151 intermediate revisions by 12 users not shown)
Line 1: Line 1:
 
__NOTOC__
 
__NOTOC__
−
=='''Co-functional networks: Organism-specific network-assisted hypothesis generation servers'''==
+
=='''CODE and DATABASE in Central Repositories'''==
 +
*[https://github.com/netbiolab Netbiolab GitHub site]
  
−
==''Animal''==
+
 
−
{|border="0"  width="800"
+
=='''Microbiome Research'''==
−
|align="center"|[[file:MouseNetLogo.png|150px|link=http://www.inetbio.org/mousenet]]
+
[[File:Hrgm logo.png|150px|link=//www.decodebiome.org/HRGM]]
−
|align="center"|[[file:WormNetv3.jpg|150px|link=http://www.inetbio.org/wormnet]]
+
'''HRGM''': A Human Reference Gut Microbiome comprising 232,098 genomes for 5414 prokaryotic species and 103 million unique proteins
−
|align="center"|[[file:Flynet.png|150px|link=http://www.inetbio.org/flynet]]
+
 
−
|align="center"|[[file:Tools_HumanNetLogo.jpg|150px|link=http://www.functionalnet.org/humannet]]
+
 
 +
[[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]]
 +
'''MRGM''': A Mouse Reference Gut Microbiome comprising 46,267 genomes for 1,689 bacterial species and 15.2 million proteins
 +
 
 +
=='''Single-cell Biology'''==
 +
[[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
 +
 
 +
[[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"|''Mus musculus''
 
|align="center"|''Mus musculus''
−
|align="center"|''Caenorhabditis elegans''
+
|align="center"|''Danio rerio''
 
|align="center"|''Drosophila melanogaster''
 
|align="center"|''Drosophila melanogaster''
−
|align="center"|''Homo sapiens''
+
|align="center"|''Caenorhabditis elegans''
 
|}
 
|}
  
−
==''Plant''==
+
==''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:RiceNetv2 logo.png|150px|link=http://www.inetbio.org/ricenet]]
+
|align="center"|[[File:Maizenet_logo_4th.png|150px|link=//www.inetbio.org/maizenet]]
 +
|align="center"|[[file:RiceNetv2 logo.png|150px|link=//www.inetbio.org/ricenet]]
 +
|align="center"|[[File:WheatNet_logo.png|150px|link=//www.inetbio.org/wheatnet]]
 +
|align="center"|[[File:BarleyNet_logo.png|150px|link=//www.inetbio.org/barleynet]]
 +
|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"|''Oryza sativa''
 
|align="center"|''Oryza sativa''
 +
|align="center"|''Triticum aestivum''
 +
|align="center"|''Hordeum vulgare''
 +
|align="center"|''Glycine max''
 +
|align="center"|''Solanum lycopersicum''
 
|}
 
|}
−
==''Microbe''==
+
 
−
{|border="0"  width="600"
+
==''Fungi''==
−
|align="center"|[[File:EcoliNet.png|150px|link=http://www.inetbio.org/ecolinet]]
+
{|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"|''Escherichia coli''
 
 
|align="center"|''Saccharomyces cerevisiae''
 
|align="center"|''Saccharomyces cerevisiae''
 
|align="center"|''Cryptococcus neoformans''
 
|align="center"|''Cryptococcus neoformans''
 
|}
 
|}
  
 +
==''Bacteria''==
 +
{|border="0"  width="200"
 +
|align="center"|[[File:Pseudomonas logo.jpg|150px|link=//www.inetbio.org/pseudomonasnet]]
 +
|align="center"|[[File:Staphnet_logo.JPG|150px|link=//www.inetbio.org/staphnet]]
 +
|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 (human pathogen)''
 +
|align="center"|Methicillin-resistant ''Staphylococcus aureus (human pathogen)''
 +
|align="center"|''Klebsiella pneumoniae (human pathogen)''
 +
|align="center"|''Escherichia coli (popular lab/factory bacterial species)''
 +
|align="center"|''Xanthomonas oryzae pv. oryzae (rice pathogen)''
 +
|}
  
−
=='''RIDDLE: Network-assisted Gene Set Analysis (human only)'''==
 
−
[[File:Cover title riddle.jpg|150px|link=http://www.functionalnet.org/riddle]] RIDDLE (Reflective diffusion and local extension) is currently available for only human genes.
 
  
 +
==''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
  
−
=='''MORPHIN: Network-assisted prediction of disease pathways in model organisms'''==
 
−
[[File:Logo morphin.png|150px|link=http://www.inetbio.org/morphin/]] Morphin (Model Organisms Projected on a Human Integrated Gene Network) is currently available.
 
  
 +
=='''Network-augmented GWAS Analysis for Arabidopsis'''==
 +
[[File:araGWAB_logo.png|150px|link=//www.inetbio.org/aragwab]]
 +
'''araGWAB''': genome-wide association boosting for ''Arabidopsis thaliana''
  
−
=='''JiffyNet:Instant gene network building server for newly sequenced species'''==
 
−
[[File:Jiffynetlogo4 small.jpg |150px|link=http://www.jiffynet.org]] Jiffy (instant) gene network modeler for newly sequenced species
 
  
 +
=='''Domain-based PPI networks by Weighted Mutual Information (WMI) '''==
 +
[[WMI|<big>'''Project Page'''</big>]]
  
−
=='''TRRUST: A reference database of human TF-target interactions'''==
 
−
[[File:TRRUST_logo.jpg |150px|link=http://www.grnpedia.org/trrust/]] TRRUST (Transcriptional Regulatory relationships Unraveled by Sentence-based Text mining) is currently available for only human genes.
 
  
−
=='''Domain-based PPI networks by Weighted Mutual Information (WMI) '''==
+
=='''Domain2Pathway by Pathway Specificity (PS) '''==
−
[[Software:WMI|To go project page]]
+
[[PS|<big>'''Project Page'''</big>]]
−
*Source codes for calculating WMI
+
−
*Yeast PPI network
+
−
*Human PPI network
+

Latest revision as of 01:03, 3 November 2025

[edit] CODE and DATABASE in Central Repositories


[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


HROM logo.png HROM: A Human Reference Oral Microbiome comprising 72,641 genomes for 3,426 prokaryotic species and 8.49 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

Retrieved from "https://netbiolab.org/wiki/index.php?title=Software&oldid=6654"
Personal tools
Namespaces

Variants
Actions
Navigation
Toolbox