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. It supports quality control, probe filtering, cell-type deconvolution, phenotype preparation, CpG-wise generalised linear models with optional term-level omnibus F tests, longitudinal mixed-effects models using 'lmerTest'/'lme4' or 'nlme', optional 'nlme' residual correlation structures, and automated reports. The workflow uses established Bioconductor tools, including 'minfi', 'ENmix', and 'wateRmelon', and runs locally or in high-performance computing environments.
Author: Paul Ruiz Pinto [aut, cre] 
Maintainer: Paul Ruiz Pinto <ruizpint at qut.edu.au>
citation("dnaEPICO")):Paul Ruiz Pinto. dnaEPICO: dnaEPICO: Analysis Pipeline for Illumina DNA Methylation Array Data. doi:10.18129/B9.bioc.dnaEPICO, R package version 0.99.38, https://bioconductor.org/packages/dnaEPICO.
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("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")| 2. Local Use of dnaEPICO | HTML | R Script |
| 1. dnaEPICO Overview | 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 | 0.99.38 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | AGPL-3 + file LICENSE |
| Depends | R (>= 4.4.0) |
| Imports | AnnotationHub, Biobase, BiocGenerics, car, RColorBrewer, data.table, ggplot2, grid, methods, minfi, openxlsx, limma, wateRmelon, ENmix, ggrepel, glm2, GenomeInfoDb, GenomicRanges, IRanges, parallel, lme4, lmerTest, nlme, quadprog, S4Vectors, SummarizedExperiment, utils, stats |
| System Requirements | Quarto command-line interface (optional, for website report generation), GNU make (optional, for Make-based workflows) |
| 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, remotes, BiocManager, BiocStyle, RefManageR, sessioninfo, devtools, testthat, ggVennDiagram, tiff, magick, knitr, rmarkdown, covr, withr, tinytex, FlowSorted.Blood.EPIC, FlowSorted.Blood.450k, BeadSorted.Saliva.EPIC, pbkrtest |
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| Enhances | |
| Depends On 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 | dnaEPICO_0.99.38.tar.gz |
| Windows Binary (x86_64) | dnaEPICO_0.99.38.zip |
| macOS Binary (big-sur-x86_64) | dnaEPICO_0.99.38.tgz |
| macOS Binary (sonoma-arm64) | dnaEPICO_0.99.38.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/dnaEPICO |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/dnaEPICO |
| Package Short Url | https://bioconductor.org/packages/dnaEPICO/ |
| Package Downloads Report | Download Stats |