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, CpG-wise generalised linear models and longitudinal mixed-effects models using 'lmerTest'/'lme4' or 'nlme', including optional 'nlme' residual correlation structures, 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.
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")| 1. dnaEPICO Overview | HTML | R Script |
| 2. Local Use of dnaEPICO | HTML | R Script |
| 3. Pipeline Use of dnaEPICO | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ChipOnChip, Epigenetics, MethylationArray, Microarray, Preprocessing, QualityControl, Software, StatisticalMethod |
| Version | 0.99.34 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | AGPL-3 + file LICENSE |
| Depends | R (>= 4.4) |
| Imports | Biobase, RColorBrewer, data.table, ggplot2, methods, minfi, openxlsx, limma, wateRmelon, ENmix, ggrepel, glm2, parallel, lme4, lmerTest, nlme, 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, AnnotationHub, 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_0.99.34.tar.gz |
| Windows Binary (x86_64) | dnaEPICO_0.99.34.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | dnaEPICO_0.99.34.tgz |
| macOS Binary (sonoma-arm64) | dnaEPICO_0.99.34.tgz |
| 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 |