GenRank: Candidate gene prioritization based on convergent evidence
Version 1.4.0

Methods for ranking genes based on convergent evidence obtained from multiple independent evidence layers. This package adapts three methods that are popular for meta-analysis.

AuthorChakravarthi Kanduri
Bioconductor views CopyNumberVariation GeneExpression Genetics Microarray SNP Sequencing Software
Date of publicationNone
MaintainerChakravarthi Kanduri <chakra.kanduri@gmail.com>
LicenseArtistic-2.0
Version1.4.0
URL https://github.com/chakri9/GenRank
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GenRank")

Getting started

Introduction to GenRank Package

Popular man pages

CombP: Convergent evidence based on combined p-values.
ComputeCE: Convergent Evidence (CE) scores of genes.
ComputeRP: Convergent evidence based on rank product method.
See all...

All man pages Function index File listing

Man pages

CombP: Convergent evidence based on combined p-values.
ComputeCE: Convergent Evidence (CE) scores of genes.
ComputeRP: Convergent evidence based on rank product method.

Functions

AddGenes Source code
CombP Man page Source code
ComputeCE Man page Source code
ComputePFP Source code
ComputeRP Man page Source code
GenPerm Source code
rankGenes Source code

Files

DESCRIPTION
NAMESPACE
R
R/add_genes.R
R/comb_pval.R
R/compute_CE.R
R/compute_RP.R
R/compute_pfp.R
R/generate_permutation_RP.R
R/rank_genes.R
build
build/vignette.rds
inst
inst/NEWS
inst/doc
inst/doc/GenRank_Vignette.R
inst/doc/GenRank_Vignette.Rmd
inst/doc/GenRank_Vignette.html
inst/extdata
inst/extdata/CE_RP_toydata.txt
inst/extdata/CE_RP_toydata_small.txt
inst/extdata/CE_toydata.txt
inst/extdata/CombP_toydata.txt
inst/extdata/CombP_toydata_small.txt
inst/extdata/RP_toydata.txt
man
man/CombP.Rd
man/ComputeCE.Rd
man/ComputeRP.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test_CombP.R
tests/testthat/test_compute_CE.R
tests/testthat/test_compute_RP.R
vignettes
vignettes/CE_scoring.pdf
vignettes/CE_scoring.png
vignettes/Figure.png
vignettes/Figure1.png
vignettes/GenRank_Vignette.Rmd
vignettes/custom.css
GenRank documentation built on May 20, 2017, 10 p.m.

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