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")):
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")
## 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")| 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 | 0.99.38 |
| 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 |
| 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_0.99.38.tar.gz |
| Windows Binary (x86_64) | dnaEPICO_0.99.36.zip (64-bit only) |
| 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/dnaEPICO/ |
| Package Short Url | https://bioconductor.org/packages/dnaEPICO/ |
| Package Downloads Report | Download Stats |