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The scripts for scientific paper titled “Integrative analysis of gene expression and DNA methylation based on the previously existing one-class logistic regression machine learning approach identifies stemness features in medulloblastoma”

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mackaay/MBpanel

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Project: MBpanel

Description:

There are the scripts for scientific article titled "Integrative analysis of gene expression and DNA methylation based on the previously existing one-class logistic regression machine learning approach identifies stemness features in medulloblastoma". The scripts are encoded using R. They can generate the result of figures and tables from the article.

Requirement:

R(https://www.r-project.org/, version >= 3.4) and R package as below:

  • biomaRt
  • caret
  • cluster
  • dplyr
  • dplyr
  • factoextra
  • forestplot
  • forestplot
  • gdata
  • gelnet
  • GGally
  • ggbeeswarm
  • ggplot2
  • ggplot2
  • ggpubr
  • ggpubr
  • glmnet
  • gridExtra
  • limma
  • NbClust
  • openxlsx
  • parallel
  • survival
  • survival
  • survivalROC
  • survivalROC
  • survminer
  • survminer
  • survMisc
  • synapseClient
  • tableone

Usage:

Please put the supplementary_append.Rdata and the *.R scripts in the same directory and change the workdir of R in the same directory.

Run the scripts:

Rscript <the R script>

Or open the R software then enter on the command line:

load("<the R script>")

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The scripts for scientific paper titled “Integrative analysis of gene expression and DNA methylation based on the previously existing one-class logistic regression machine learning approach identifies stemness features in medulloblastoma”

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