COHCAP (City of Hope CpG Island Analysis Pipeline) is an algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values.
If you use COHCAP please cite:
Charles D. Warden, Heehyoung Lee, Joshua D. Tompkins, Xiaojin Li, Charles Wang, Arthur D. Riggs, Hua Yu, Richard Jove, Yate-Ching Yuan. (2013) COHCAP: An Integrative Genomic Pipeline for Single-Nucleotide Resolution DNA Methylation Analysis. Nucleic Acids Research. 41 (11): e117
- DNA methylation analysis
- integration of methylation and gene expression data
- graphical user interface for basic users
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