th86 / gislkit

GISL Toolkit

gislkit

Installation

We can install Gislkit using the following commands:

#install.packages("devtools")
library(devtools)
install_github("th86/gislkit")

If you encounter the error messages about RCurl, installing the following packages may fix the problem.

sudo apt-get install libcurl4-openssl-dev libssl-dev libxml2-dev

Usage

To find the attractors in a gene expression matrix ge using CENPA, PTPRC, COL3A1 as seeds:

attractorList<-attractorSearch(ge, c("CENPA","PTPRC","COL3A1"))

The function returns a list of converged attractors.

To find all the genomically localized attractors in a gene expression matrix:

data(grch37.geneSymbol)
GLattractorList<-GLattractorSearch(ge,genome=grch37_genesymbol)

The function returns a list of converged genomically localized attractors.