README.md

SCEM (Stemness Calculation for gene Expression or Methylation data) package

The goal of SCEM is to calculate stemness score from gene expression or methylation data. I wrapped some functions from "Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation". Original workflow is at https://bioinformaticsfmrp.github.io/PanCanStem_Web/.

Installation

remotes::install_github("Byronxy/SCEM")

Example

Input: Gene expression matrix (Row: Symbal ID, Column: Sample ID) or DNA methylation matrix (Row: Probe ID, Column: Sample ID)

library(SCEM)
rnascore <- getRNAstemness(expr = expr)
dnascore <- getDNAstemness(expr = expr)