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.

AuthorCharles Warden
Date of publicationNone
MaintainerCharles Warden <cwarden45@gmail.com>
LicenseGPL-3
Version1.16.0

View on Bioconductor

Files in this package

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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