dnaEPICO
This is the development version of dnaEPICO; to use it, please install the devel version of Bioconductor.
dnaEPICO: Analysis Pipeline for Illumina DNA Methylation Array Data
Bioconductor version: Development (3.24)
A modular and reproducible workflow for preprocessing and analysing Illumina DNA methylation array data from the EPICv2, EPIC, and 450K platforms. The package integrates quality control, probe filtering, cell-type deconvolution, phenotype preparation, generalised linear models, linear mixed-effects models, and automated report generation. It builds on established Bioconductor infrastructure and wraps commonly used tools including 'minfi', 'ENmix', and 'wateRmelon', with support for both local execution and high-performance computing workflows.
Author: Paul Ruiz [aut, cre]
, Divya Mehta [aut]
Maintainer: Paul Ruiz <ruizpint at qut.edu.au>
citation("dnaEPICO")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("dnaEPICO")
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("dnaEPICO")| File-Based and Pipeline Use of dnaEPICO | HTML | R Script |
| Interactive Local Use of dnaEPICO | HTML | R Script |
| Reference Manual |
Details
| biocViews | ChipOnChip, Epigenetics, MethylationArray, Microarray, Preprocessing, QualityControl, Software, StatisticalMethod |
| Version | 0.99.17 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | AGPL-3 + file LICENSE |
| Depends | R (>= 4.4) |
| Imports | Biobase, RColorBrewer, data.table, ggplot2, MASS, methods, minfi, limma, wateRmelon, ENmix, ggrepel, glm2, parallel, lme4, lmerTest, quadprog, SummarizedExperiment, utils, stats |
| System Requirements | |
| URL | https://github.com/paulYRP/dnaEPICO |
| Bug Reports | https://github.com/paulYRP/dnaEPICO/issues |
See More
| Suggests | IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICv2anno.20a1.hg38, IlluminaHumanMethylationEPICv2manifest, IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, minfiData, GenomicRanges, S4Vectors, remotes, BiocManager, BiocStyle, RefManageR, sessioninfo, devtools, testthat, tiff, magick, knitr, rmarkdown, covr, withr, tinytex, FlowSorted.Blood.EPIC, FlowSorted.Blood.450k, BeadSorted.Saliva.EPIC |
| 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 | dnaEPICO_0.99.17.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/dnaEPICO |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/dnaEPICO |
| Bioc Package Browser | https://code.bioconductor.org/browse/dnaEPICO/ |
| Package Short Url | https://bioconductor.org/packages/dnaEPICO/ |
| Package Downloads Report | Download Stats |