methylCC

This is the development version of methylCC; for the stable release version, see methylCC.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10

Estimate the cell composition of whole blood in DNA methylation samples

Bioconductor version: Development (3.24)

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] ORCID: 0000-0002-7858-0231 , Rafael Irizarry [aut] ORCID: 0000-0002-3944-4309

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

Citation (from within R, enter citation("methylCC")):

Stephanie C. Hicks, Rafael Irizarry. methylCC: Estimate the cell composition of whole blood in DNA methylation samples. doi:10.18129/B9.bioc.methylCC, R package version 1.27.0, https://bioconductor.org/packages/methylCC.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DNAMethylation, MethylSeq, MethylationArray, Microarray, Sequencing, Software, WholeGenome
Version	1.27.0
In Bioconductor since	BioC 3.10 (R-3.6) (7 years)
License	GPL-3
Depends	R (>= 3.6), FlowSorted.Blood.450k
Imports	Biobase, GenomicRanges, IRanges, S4Vectors, dplyr, magrittr, minfi, bsseq, quadprog, stats, utils, bumphunter, genefilter, methods, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19
System Requirements
URL	https://github.com/stephaniehicks/methylCC/
Bug Reports	https://github.com/stephaniehicks/methylCC/

Suggests	rmarkdown, knitr, testthat (>= 2.1.0), BiocGenerics, BiocStyle, tidyr, ggplot2
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
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Build Report	Build Report, r-universe

Package Archives

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

Source Package	methylCC_1.27.0.tar.gz
Windows Binary (x86_64)	methylCC_1.27.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	methylCC_1.27.0.tgz
macOS Binary (sonoma-arm64)	methylCC_1.27.0.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