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DESCRIPTION
GScluster.Rproj 6th commit Jan 2, 2019
GScluster_manual_v1.1.6.pdf
NAMESPACE
README.md
sample_genescore.txt
sample_genescore2.txt
sample_genescore3.txt
sample_geneset.txt GSA result file for T2D GWAS data Mar 15, 2019
sample_geneset2.txt
sample_geneset3.txt

README.md

GScluster is a standalone Shiny/R package for network-weighted gene-set clustering and network visualization.

Installation

Open R program and type following commands in R console.

install.packages('devtools')
library(devtools)
install_github('unistbig/GScluster')
library(GScluster)

Example Run

To run demo file, please type following R code.

GScluster()

To run user's own data, please modify following example R codes.

  1. Read gene-set analysis result table.

GSAresult=read.delim('https://github.com/unistbig/GScluster/raw/master/sample_geneset.txt', stringsAsFactors=FALSE)

  1. Read gene score table.

GeneScores=read.delim('https://github.com/unistbig/GScluster/raw/master/sample_genescore.txt', header=F)

  1. Run GScluster

GScluster(GSAresult = GSAresult, GeneScores = GeneScores, Species = 'H', alpha = 1, GsQCutoff = 0.25, GQCutoff = 0.05)

User's Manual

User's manual is available here.

Example data download


Running time of GScluster is shown below for different numbers of input gene-sets.


Contact: Dougu Nam (dougnam@unist.ac.kr)
Any feedback or comments are greatly appreciated!!

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