COHCAP: CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("COHCAP")
AuthorCharles Warden
Bioconductor views DNAMethylation DifferentialMethylation Epigenetics MethylSeq Microarray
Date of publicationNone
MaintainerCharles Warden <cwarden45@gmail.com>
LicenseGPL-3
Version1.20.0

View on Bioconductor

Files

CHANGES
DESCRIPTION
NAMESPACE
R
R/COHCAP.BSSeq.preprocess.R R/COHCAP.annotate.R R/COHCAP.avg.by.island.R R/COHCAP.avg.by.site.R R/COHCAP.denovo.R R/COHCAP.integrate.avg.by.island.R R/COHCAP.integrate.avg.by.site.R R/COHCAP.qc.R R/COHCAP.site.R
build
build/vignette.rds
inst
inst/CITATION
inst/Perl
inst/Perl/create_wig_files.pl
inst/Perl/find_bismark_CpG_sites.pl
inst/Perl/integrate_island.pl
inst/Perl/integrate_site.pl
inst/doc
inst/doc/COHCAP.R
inst/doc/COHCAP.Rnw
inst/doc/COHCAP.pdf
inst/extdata
inst/extdata/BSSeq
inst/extdata/BSSeq/HCT116_truncated.bed
inst/extdata/GENCODE_Genes_truncated.bed
inst/extdata/GSE42308_truncated.txt
inst/extdata/UCSC_CpG_Islands_truncated.bed
inst/extdata/expression-Average_by_Island_truncated.txt
inst/extdata/expression-Average_by_Site_truncated.txt
inst/extdata/sample_GSE42308.txt
man
man/COHCAP.BSSeq.preprocess.Rd man/COHCAP.annotate.Rd man/COHCAP.avg.by.island.Rd man/COHCAP.avg.by.site.Rd man/COHCAP.denovo.Rd man/COHCAP.integrate.avg.by.island.Rd man/COHCAP.integrate.avg.by.site.Rd man/COHCAP.qc.Rd man/COHCAP.site.Rd
vignettes
vignettes/COHCAP.Rnw

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