scholarly journals GenRank: an R/Bioconductor package for prioritization of candidate genes

2016 ◽  
Author(s):  
Chakravarthi Kanduri ◽  
Irma Järvelä

AbstractSummary:Modern high-throughput studies often yield long lists of genes, of which a fraction are of high relevance to the phenotype of interest. To prioritize the candidate genes of complex genetic traits, our R/Bioconductor package GenRank provides methods that are based on convergent evidence obtained from multiple independent evidence layers. The package facilitates an extensible framework that allows a further addition of novel methods for candidate gene prioritization.Availability and Implementation:The methods are implemented in R and available as a package in Bioconductor repository (http://bioconductor.org/packages/GenRank/).Contact:[email protected]

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 463
Author(s):  
Chakravarthi Kanduri ◽  
Irma Järvelä

Modern high-throughput studies often yield long lists of genes, a fraction of which are of high relevance to the phenotype of interest. To prioritize the candidate genes of complex genetic traits, our R/Bioconductor package GenRank ranks genes based on convergent evidence obtained from multiple layers of independent evidence. We implemented three methods to rank genes that integrate gene-level data generated from multiple layers of evidence: (a) the convergent evidence (CE) method aggregates evidence based on a weighted vote counting method; (b) the rank product (RP) method performs a meta-analysis of microarray-based gene expression data, and (c) the traditional method combines p-values. The methods are implemented in R and are available as a package in the Bioconductor repository (http://bioconductor.org/packages/GenRank/).


2010 ◽  
Vol 26 (18) ◽  
pp. i618-i624 ◽  
Author(s):  
Rosario M. Piro ◽  
Ivan Molineris ◽  
Ugo Ala ◽  
Paolo Provero ◽  
Ferdinando Di Cunto

2012 ◽  
Vol 287 (9) ◽  
pp. 679-698 ◽  
Author(s):  
Ali Masoudi-Nejad ◽  
Alireza Meshkin ◽  
Behzad Haji-Eghrari ◽  
Gholamreza Bidkhori

2010 ◽  
Vol 8 (8) ◽  
pp. 1869-1871 ◽  
Author(s):  
C. Y. VOSSEN ◽  
C. C. ELBERS ◽  
B. P. C. KOELEMAN ◽  
F. R. ROSENDAAL ◽  
E. G. BOVILL

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