ISCindex

An R package to calculate an intestinal stem cell index from gene expression profiling data

The ISCindex R package provides a function to calculate an intestinal stem cell index describing stem cell phenotype along a continuum from a more conventional Crypt Base Columnar stem cell (CBC) to a Regenerative Stem Cell (RSC) phenotype.

If you use ISCindex in your work, please cite the following paper:

Gil Vazquez et al. Dynamic and adaptive cancer stem cell population admixture in colorectal neoplasia. Cell Stem Cell, Volume 29, Issue 8, 1213 - 1228.e8

Installation

The package can be installed in R by entering the following commands:

if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")
devtools::install_github("gnvalbuena/ISCindex")

UPDATE: This version has been updated for functions to conform with backend changes in the GSVA package from version 1.52.3. There are no changes to how the package function is used.

Usage

To calculate the stem cell index, use

stemcellindex(geneexpressiondata, organism, geneid)

where

• geneexpressiondata is a table of gene expression data (microarray or RNAseq), with genes in rows and samples in columns
• organism is either "mouse" or "human"
• geneid is the type of gene identifiers in the rownames of geneexpreessiondata, either "ensembl" or "genename"

The function will return a data frame containing

• RSC - single sample Regenerative Stem Cell scores
• CBC - single sample Crypt Base Columnar Stem Cell scores
• stemcellindex - stem cell index

Access the manual for the stemcellindex function by entering ?stemcellindex