methylCC

DOI: 10.18129/B9.bioc.methylCC    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see methylCC.

Estimate the cell composition of whole blood in DNA methylation samples

Bioconductor version: 3.13

A tool to estimate the cell composition of DNA methylation whole blood sample measured on any platform technology (microarray and sequencing).

Author: Stephanie C. Hicks [aut, cre] , Rafael Irizarry [aut]

Maintainer: Stephanie C. Hicks <shicks19 at jhu.edu>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("methylCC")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("methylCC")

 

HTML	R Script	The methylCC user's guide
PDF		Reference Manual
Text		NEWS

Details

biocViews	DNAMethylation, MethylSeq, MethylationArray, Microarray, Sequencing, Software, WholeGenome
Version	1.6.0
In Bioconductor since	BioC 3.10 (R-3.6) (2 years)
License	CC BY 4.0
Depends	R (>= 3.6), FlowSorted.Blood.450k
Imports	Biobase, GenomicRanges, IRanges, S4Vectors, dplyr, magrittr, minfi, bsseq, quadprog, plyranges, stats, utils, bumphunter, genefilter, methods, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19
LinkingTo
Suggests	knitr, testthat (>= 2.1.0), BiocGenerics, BiocStyle, tidyr, ggplot2
SystemRequirements
Enhances
URL	https://github.com/stephaniehicks/methylCC/
BugReports	https://github.com/stephaniehicks/methylCC/
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	methylCC_1.6.0.tar.gz
Windows Binary	methylCC_1.6.0.zip
macOS 10.13 (High Sierra)	methylCC_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/methylCC
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/methylCC
Package Short Url	https://bioconductor.org/packages/methylCC/
Package Downloads Report	Download Stats