:: DESCRIPTION
VPMBench automates the evaluation of variant prioritization methods by using a pipeline in which the methods are integrated as plugins.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Ruscheinski A, Reimler AL, Ewald R, Uhrmacher AM.
VPMBench: a test bench for variant prioritization methods.
BMC Bioinformatics. 2021 Nov 8;22(1):543. doi: 10.1186/s12859-021-04458-0. PMID: 34749640.
:: DESCRIPTION
RAP is a rank aggregation-based data fusion approach for gene prioritization in plants. It can be used to perform the gene prioritization in Arabidopsis thaliana and 28 non-plant species.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhai J, Tang Y, Yuan H, Wang L, Shang H, Ma C.
A Meta-Analysis Based Method for Prioritizing Candidate Genes Involved in a Pre-specific Function.
Front Plant Sci. 2016 Dec 15;7:1914. doi: 10.3389/fpls.2016.01914. PMID: 28018423; PMCID: PMC5156684.
:: DESCRIPTION
ChroMoS (Chromatin Modified SNPs) combines genetic and epigenetic data to facilitate SNP classification, prioritization and prediction of their functional effect.
::DEVELOPER
Bioinformatics and Next Generation Sequencing Group; Max Planck Institute of Immunobiology and Epigenetics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: 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.
:: DESCRIPTION
maxLRc is a likelihood ratio-based measure for the statistical component of ranking rare variants under a case-control study design that avoids the hypothesis-testing paradigm.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Li W, Dobbins S, Tomlinson I, Houlston R, Pal DK, Strug LJ.
Prioritizing rare variants with conditional likelihood ratios.
Hum Hered. 2015;79(1):5-13. doi: 10.1159/000371579. Epub 2015 Feb 3. PMID: 25659987; PMCID: PMC4759929.
:: 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
:: DOWNLOAD
:: 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.
:: DESCRIPTION
mirTarPri is a web toolkit for prioritising candidate mirRNA targets in the context of functional genomic data.
::DEVELOPER
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: 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.
:: 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
:: DOWNLOAD
:: 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.
:: DESCRIPTION
NetworkPrioritizer provides multiple features to rank individual nodes based on centrality measures according to their relevance to the rest of the network. This can be accomplished either globally or locally with regard to a set of seed nodes. The global approach is basically a standard centrality analysis, whereas the local approach reveals how important individual nodes are for the connections between the set of seed nodes and the rest of the network. A frequent application of NetworkPrioritizer is the prioritization of candidate disease genes. Here, genes known for a given disease constitute the seed set, and the nodes top-ranked as a result of applying NetworkPrioritizer are identified as promising putative disease genes. NetworkPrioritizer can be applied to both directed and undirected networks. It will, however, treat all edges as undirected for the centrality computations. Apart from the computation of centrality measures NetworkPrioritizer also offers useful tools for the comparison and aggregation of multiple rankings.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 Jun 1;29(11):1471-3. doi: 10.1093/bioinformatics/btt164. Epub 2013 Apr 16.
NetworkPrioritizer: a versatile tool for network-based prioritization of candidate disease genes or other molecules.
Kacprowski T1, Doncheva NT, Albrecht M.
:: DESCRIPTION
Endeavour is a software application for the computational prioritization of candidates genes, based on a set of training genes. It is made up of three stages: training, scoring and fusion. In the first stage, information about the training genes (genes already known to play a role in the process under study) are retrieved from numerous data sources in order to build models. It includes functionnal annotations, protein-protein interactions, regulatory information, expression data, sequence based data and literature mining data. In the second stage, the models are then used to score the candidate genes and to rank them according to their scores. Lastly, the rankings per data source are fused into a global ranking using order statistics. Endeavour is available for human, mouse, rat, fruit fly and worm.
::DEVELOPER
The Bioinformatics Research Group
:: SCREENSHOTS
:: REQUIREMENTS
:: MORE INFORMATION
Citation
Tranchevent L., Barriot R., Yu S., Van Vooren S., Van Loo P., Coessens B., Aerts S., De Moor B., Moreau Y.,
“ENDEAVOUR update: a web resource for gene prioritization in multiple species“,
Nucl. Acids Res. (2008) 36 (suppl 2): W377-W384.
Aerts S, Vilain S, Hu S, Tranchevent L-C, Barriot R, et al. (2009)
“Integrating large scale bioinformatics and forward genetics in Drosophila“.
PLoS Genet 5(1): e1000351. doi:10.1371/journal.pgen.1000351
:: 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
:: 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.
