PheGenEx 3.0 – Phenome-Genome Explorer

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May 272016
 

PheGenEx 3.0

:: DESCRIPTION

PheGenEx is a realtime webtool for prediction, network-based analysis and visualization of phenotype-gene associations in the context of human diseases.

::DEVELOPER

KUANG LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  rcNet

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Oct 1;27(19):2692-9. doi: 10.1093/bioinformatics/btr463. Epub 2011 Aug 8.
Inferring disease and gene set associations with rank coherence in networks.
Hwang T1, Zhang W, Xie M, Liu J, Kuang R.

Net-RSTQ – Network-based method for RNA-Seq-based Transcript Quantification

 Miscellaneous 5 views Comments Off on Net-RSTQ – Network-based method for RNA-Seq-based Transcript Quantification
May 272016
 
Net-RSTQ - Network-based method for RNA-Seq-based Transcript Quantification

Net-RSTQ :: DESCRIPTION Net-RSTQ is a software to integrate protein domain-domain interaction network with short read alignments for transcript abundance estimation. ::DEVELOPER KUANG LAB :: SCREENSHOTS N/A :: REQUIREMENTS Windows/Linux MatLab :: DOWNLOAD  Net-RSTQ :: MORE INFORMATION Citation Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis. Zhang W, Chang JW, Lin L, Minn […]

MFlux – Rapid Prediction of Bacterial Heterotrophic Fluxomics

 System Biology & Modeling 0 views Comments Off on MFlux – Rapid Prediction of Bacterial Heterotrophic Fluxomics
May 272016
 
MFlux - Rapid Prediction of Bacterial Heterotrophic Fluxomics

MFlux :: DESCRIPTION MFlux is a web-based platform that predicts the bacterial central metabolism via machine learning, leveraging data from approximately 100 13C-MFA papers on heterotrophic bacterial metabolisms. ::DEVELOPER MFlux team :: SCREENSHOTS N/A :: REQUIREMENTS Web browser :: DOWNLOAD  NO :: MORE INFORMATION Citation Rapid Prediction of Bacterial Heterotrophic Fluxomics Using Machine Learning and […]

visANT 5.50 – Integrative Visual Analysis Tool for Biological Networks & Pathways

 System Biology & Modeling 783 views Comments Off on visANT 5.50 – Integrative Visual Analysis Tool for Biological Networks & Pathways
May 272016
 
visANT 5.50 - Integrative Visual Analysis Tool for Biological Networks & Pathways

visANT 5.50 :: DESCRIPTION visANT is an integrative visual analysis tool for biological networks and pathways. VisANT is implemented as a java applet which can be run in most common browsers and has been test with Netscape, Internet Explorer with different versions on different platforms. ::DEVELOPER VisANT Team :: SCREENSHOTS :: REQUIREMENTS Windows/ Linux JAVA :: […]

DCF 0.6 – Peptide Design by Compatible Functions

 Protein Sequence Analysis 1 views Comments Off on DCF 0.6 – Peptide Design by Compatible Functions
May 272016
 
DCF 0.6 - Peptide Design by Compatible Functions

DCF 0.6 :: DESCRIPTION DCF (Design by Compatible Functions) is a peptide design principle for multifunctional peptides based on similarity to a functional reference class. ::DEVELOPER the IROnBioS Group :: SCREENSHOTS N/A :: REQUIREMENTS Linux :: DOWNLOAD  DCF :: MORE INFORMATION Citation Effective Design of Multifunctional Peptides by Combining Compatible Functions. Diener C, Garza Ramos […]

PRISM 2.0 – Prediction of Protein-protein Interactions and Modeling their 3D Complexes

 3D molecular model 3 views Comments Off on PRISM 2.0 – Prediction of Protein-protein Interactions and Modeling their 3D Complexes
May 272016
 
PRISM 2.0 - Prediction of Protein-protein Interactions and Modeling their 3D Complexes

PRISM 2.0 :: DESCRIPTION The PRISM web server enables fast and accurate prediction of protein-protein interactions (PPIs). ::DEVELOPER the COSBI (Computational Systems Biology) group :: SCREENSHOTS N/A :: REQUIREMENTS Linux Python :: DOWNLOAD PRISM PROTOCOL :: MORE INFORMATION Citation Baspinar A, Cukuroglu E, Nussinov R, Keskin O, Gursoy A. PRISM: A web server and repository […]

HotPoint – Hot Spot Prediction Server for Protein Interfaces

 Protein Sequence Analysis 4 views Comments Off on HotPoint – Hot Spot Prediction Server for Protein Interfaces
May 272016
 
HotPoint - Hot Spot Prediction Server for Protein Interfaces

HotPoint :: DESCRIPTION HotPoint is a web server which predicts hot spots in protein interfaces using an empirical model. ::DEVELOPER the COSBI (Computational Systems Biology) group :: SCREENSHOTS N/A :: REQUIREMENTS Web browser :: DOWNLOAD  NO :: MORE INFORMATION Citation HotPoint: hot spot prediction server for protein interfaces. Tuncbag N, Keskin O, Gursoy A. Nucleic […]

Omics Integrator 0.2 – Python Scripts for Analyzing Diverse Forms of ‘omic’ data

 Miscellaneous 3 views Comments Off on Omics Integrator 0.2 – Python Scripts for Analyzing Diverse Forms of ‘omic’ data
May 272016
 
Omics Integrator 0.2 - Python Scripts for Analyzing Diverse Forms of 'omic' data

Omics Integrator 0.2 :: DESCRIPTION Omics Integrator is package comprised of command-line tools designed to integrate high-throughput datasets such as gene expression, phospho-proteomic data and the results from genetic screens. ::DEVELOPER The Fraenkel Lab :: SCREENSHOTS N/A :: REQUIREMENTS Linux Python :: DOWNLOAD   Omics Integrator :: MORE INFORMATION Citation Network-Based Interpretation of Diverse High-Throughput Datasets […]

Cocos – Reconstructing Phylogenies of Multi-Domain Proteins

 Phylogenetic Analysis 1 views Comments Off on Cocos – Reconstructing Phylogenies of Multi-Domain Proteins
May 272016
 
Cocos - Reconstructing Phylogenies of Multi-Domain Proteins

Cocos :: DESCRIPTION Cocos is a tool to construct phylogenies of multi-domain proteins. ::DEVELOPER Research Group Microbial Virulence :: SCREENSHOTS N/A :: REQUIREMENTS Linux / Windows Python :: DOWNLOAD  Cocos :: MORE INFORMATION Citation Cocos: Constructing multi-domain protein phylogenies. Homilius M, Wiedenhoeft J, Thieme S, Standfuß C, Kel I, Krause R. PLoS Curr. 2011 Jun […]

HaMMLET – Fast Bayesian Hidden Markov Model with Wavelet Compression

 Miscellaneous 1 views Comments Off on HaMMLET – Fast Bayesian Hidden Markov Model with Wavelet Compression
May 272016
 
HaMMLET - Fast Bayesian Hidden Markov Model with Wavelet Compression

HaMMLET :: DESCRIPTION HaMMLET is a fast Forward-Backward Gibbs sampler for Bayesian inference on Hidden Markov Models (HMM). It uses the Haar wavelet transform to dynamically compress the data based on the current variance sample in each iteration. ::DEVELOPER Schliep lab :: SCREENSHOTS N/A :: REQUIREMENTS Linux GCC :: DOWNLOAD  HaMMLET :: MORE INFORMATION Citation […]