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

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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.

Author
Charles Warden
Date of publication
None
Maintainer
Charles Warden <cwarden45@gmail.com>
License
GPL-3
Version
1.16.0

View on Bioconductor

Man pages

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

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