methylCC
This is the released version of methylCC; for the devel version, see methylCC.
Estimate the cell composition of whole blood in DNA methylation samples
Bioconductor version: Release (3.23)
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>
citation("methylCC")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("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")| The methylCC user's guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, MethylSeq, MethylationArray, Microarray, Sequencing, Software, WholeGenome |
| Version | 1.26.0 |
| 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/ |
See More
| Suggests | rmarkdown, knitr, testthat (>= 2.1.0), BiocGenerics, BiocStyle, tidyr, ggplot2 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | methylCC_1.26.0.tar.gz |
| Windows Binary (x86_64) | methylCC_1.26.0.zip |
| macOS Binary (big-sur-x86_64) | methylCC_1.26.0.tgz |
| macOS Binary (sonoma-arm64) | methylCC_1.26.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/methylCC |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/methylCC |
| Bioc Package Browser | https://code.bioconductor.org/browse/methylCC/ |
| Package Short Url | https://bioconductor.org/packages/methylCC/ |
| Package Downloads Report | Download Stats |