This package provides a pipeline to analyze single-nucleotide resolution methylation data (Illumina 450k/EPIC methylation array, targeted BS-Seq, etc.). It provides differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, with visualizaton options.
|Bioconductor views||DNAMethylation DifferentialMethylation Epigenetics MethylSeq Microarray|
|Date of publication||None|
|Maintainer||Charles Warden <email@example.com>|
COHCAP.annotate: Annotation for CpG Sites
COHCAP.avg.by.island: CpG Island Differential Methylation Analysis (Average by...
COHCAP.avg.by.site: CpG Island Differential Methylation Analysis (Average by Site...
COHCAP.BSSeq.preprocess: Preprocessing for Targeted BS-Seq data
COHCAP.denovo: De-Novo Identification of Differentially Methylated CpG Site...
COHCAP.integrate.avg.by.island: Integration with Gene Expression Data(Average by Island...
COHCAP.integrate.avg.by.site: Integration with Gene Expression Data(Average by Site...
COHCAP.qc: DNA Methylation Quality Control Statistics
COHCAP.site: CpG Site Differential Methylation Analysis
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