FlyNet – Versatile Network Prioritization server for Drosophila Melanogaster

FlyNet

:: DESCRIPTION

FlyNet is a network prioritization server for the Drosophila melanogaster biology. The FlyNet web server is specialized for the generation of versatile hypothesis in Drosophila-based studies.

::DEVELOPER

NetBioLab, Yonsei University, Seoul, Korea.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

FlyNet: a versatile network prioritization server for the Drosophila community.
Shin J, Yang S, Kim E, Kim CY, Shim H, Cho A, Kim H, Hwang S, Shim JE, Lee I.
Nucleic Acids Res. 2015 Jul 1;43(W1):W91-7. doi: 10.1093/nar/gkv453.

RVboost 0.1 – RNA-seq Variant Prioritization approach for Illumina Next-generation Sequencing data

RVboost 0.1

:: DESCRIPTION

RVboost is a novel method specific for RNA variant prioritization.

::DEVELOPER

RVboost team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RVboost

:: MORE INFORMATION

Citation

RVboost: RNA-Seq variants prioritization using a boosting method.
Wang C, Davila JI, Baheti S, Bhagwate AV, Wang X, Kocher JP, Slager SL, Feldman AL, Novak AJ, Cerhan JR, Thompson EA, Asmann YW.
Bioinformatics. 2014 Aug 27. pii: btu577

CancerDP – Prioritization of Anticancer Drugs

CancerDP

:: DESCRIPTION

CancerDP is a web server for predicting priority/potency of an anticancer drug against a cancer cell line using its genomic features

::DEVELOPER

CancerDP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Prioritization of anticancer drugs against a cancer using genomic features of cancer cells: A step towards personalized medicine.
Gupta S, Chaudhary K, Kumar R, Gautam A, Nanda JS, Dhanda SK, Brahmachari SK, Raghava GP.
Sci Rep. 2016 Mar 31;6:23857. doi: 10.1038/srep23857.

ProDiGe 0.3 – Prioritization of Disease Genes

ProDiGe 0.3

:: DESCRIPTION

ProDiGe is a free MATLAB implementation of an algorithm for gene prioritization or gene ranking.

::DEVELOPER

Centre for Computational Biology

:: SCREENSHOTS

 N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • MATLAB

:: DOWNLOAD

 ProDiGe

:: MORE INFORMATION

Citation

F. Mordelet and J.-P. Vert.
ProDiGe: PRioritization Of Disease Genes with multitask machine learning from positive and unlabeled examples.
BMC Bioinformatics 2011, 12:389.

ExomeWalker – Prioritization of Whole-exome data by Random-walk analysis of Protein-protein interactions

ExomeWalker

:: DESCRIPTION

EXOME WALKER is a computational method to prioritise a set of candidates in exome sequencing projects that aim to identify novel Mendelian disease genes.

::DEVELOPER

The Computational Biology @ Charité Berlin at the Institute for Medical Genetics and Human Genetics at Charité-Universitätsmedizin Berlin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Walking the interactome for candidate prioritization in exome sequencing studies of Mendelian diseases.
Smedley D, Köhler S, Czeschik JC, Amberger J, Bocchini C, Hamosh A, Veldboer J, Zemojtel T, Robinson PN.
Bioinformatics. 2014 Jul 30. pii: btu508.

mirTarPri 1.0alpha – miRNA Target Prioritization method

mirTarPri 1.0alpha

:: DESCRIPTION

mirTarPri is a web toolkit for prioritising candidate mirRNA targets in the context of functional genomic data.

::DEVELOPER

mirTarPri team

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

PLoS One. 2013;8(1):e53685. doi: 10.1371/journal.pone.0053685. Epub 2013 Jan 9.
mirTarPri: improved prioritization of microRNA targets through incorporation of functional genomics data.
Wang P1, Ning S, Wang Q, Li R, Ye J, Zhao Z, Li Y, Huang T, Li X.

snvForest 14.07.31 – Prioritization of Nonsynonymous SNV via Integrative Learning on multiple Genomic data

snvForest 14.07.31

:: DESCRIPTION

snvForest, meaning , is a bioinformatics tool for prioritizing candidate nonsynonymous SNV. In this tool, we propose an integrative learning model that integrates one type of phenotype similarity, eight types of gene similarities and eleven types of variant fuctional predictions to prioritize disease-causing nonsynonymous SNV.

:: DEVELOPER

RUI Jiang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows

:: DOWNLOAD

 snvForest

:: MORE INFORMATION

Citation

Mengmeng Wu, Jiaxin Wu, Ting Chen, Rui Jiang
Prioritization of nonsynonymous single nucleotide variants for exome sequencing studies via integrative learning on multiple genomic data,
in submission, 2015.

EPSILON – eQTL Prioritization using Similarity Measures derived from Local Interaction Networks

EPSILON

:: DESCRIPTION

EPSILON is an extendable framework for eQTL prioritization, which mitigates the effect of highly connected genes and unreliable interactions by constructing a local network before a network-based similarity measure is applied to select the true causal gene.

::DEVELOPER

Lieven P.C. Verbeke lieven.verbeke@intec.ugent.be or jan.fostier@intec.ugent.be

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Matlab/C++

:: DOWNLOAD

  EPSILON

:: MORE INFORMATION

Citation:

Lieven P. C. Verbeke; Lore Cloots; Piet Demeester; Jan Fostier; Kathleen Marchal
EPSILON: an eQTL prioritization framework using similarity measures derived from local networks
Bioinformatics (2013) 29 (10): 1308-1316.

BiERapp 1.4.2 – Gene/Variant Prioritization tool

BiERapp 1.4.2

:: DESCRIPTION

BiERapp ( BioInformatic for Rare Diseases Application) allows finding genes affected by deleterious variants that segregate along family pedigrees , case-controls or sporadic samples .

::DEVELOPER

Bioinformatics and Genomics Department at CIPF

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • HTML5 and Javascript

:: DOWNLOAD

 BiERapp

:: MORE INFORMATION

Citation

A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies.
Alemán A, Garcia-Garcia F, Salavert F, Medina I, Dopazo J.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W88-93. doi: 10.1093/nar/gku407.

ChroMoS – SNP Classification, Prioritization and Functional Interpretation

ChroMoS

:: DESCRIPTION

ChroMoS (Chromatin Modified SNPs) combines genetic and epigenetic data to facilitate SNP classification, prioritization and prediction of their functional effect.

::DEVELOPER

epicenter – bioinformatic group of MPIIE (Max-Planck Institute of Immunobiology and Epigenetics,)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ChroMoS: an integrated web tool for SNP classification, prioritization and functional interpretation.
Barenboim M, Manke T.
Bioinformatics. 2013 Sep 1;29(17):2197-8. doi: 10.1093/bioinformatics/btt356.