CanMethdb: a database for genome-wide DNA methylation annotation in cancers

Table of contents AND pipline

• [NearGenes](# Get candidate genes for each CpG)
  1. NearGenes.R
  2. run_NearGene.R
• [Common samples](# Get DNA methylation and gene expression profiles of common samples)
  1. profiles_com_sample.py
• [Data pre-processing]
  1. gene_profile_pre-processing.py
  2. methylation_profile_pre-processing.py
• [ELMER](# Use ElMER method to calculate target genes for each CpG in each cancer type)
  1. EMLMER.R
  2. run_ELMER.R
• [Pearson](# Use Pearson’s correlation coefficient method to calculate target genes for each CpG in each cancer type )
  1. pearson.py
• [limma](# Use limma to find differentially methylated CpGs)
  1. limma.R

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