recountmethylation
Access and analyze public DNA methylation array data compilations
Bioconductor version: 3.23 · Package version: 1.22.0
Resources for cross-study analyses of public DNAm array data from NCBI GEO repo, produced using Illumina's Infinium HumanMethylation450K (HM450K) and MethylationEPIC (EPIC) platforms. Provided functions enable download, summary, and filtering of large compilation files. Vignettes detail background about file formats, example analyses, and more. Note the disclaimer on package load and consult the main manuscripts for further info.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("recountmethylation")Details
| Maintainer | Sean K Maden <maden@ohsu.edu> |
| Author | Sean K Maden [cre, aut] (ORCID: <https://orcid.org/0000-0002-2212-4894>), Brian Walsh [aut] (ORCID: <https://orcid.org/0000-0003-0913-1528>), Kyle Ellrott [aut] (ORCID: <https://orcid.org/0000-0002-6573-5900>), Kasper D Hansen [aut] (ORCID: <https://orcid.org/0000-0003-0086-0687>), Reid F Thompson [aut] (ORCID: <https://orcid.org/0000-0003-3661-5296>), Abhinav Nellore [aut] (ORCID: <https://orcid.org/0000-0001-8145-1484>) |
| License | Artistic-2.0 |
| URL | https://github.com/metamaden/recountmethylation |
| Bug Reports | https://github.com/metamaden/recountmethylation/issues |
| Downloads rank | 532 |
| Source branch | RELEASE_3_23 |
| biocViews | DNAMethylation, Epigenetics, ExperimentHub, MethylationArray, Microarray, Software |
Documentation
- Data Analyses
- Determine population ancestry from DNAm arrays
- Nearest neighbors analysis for DNAm arrays
- Power analysis for DNAm arrays
- Practical uses for provided CpG probe annotations
- recountmethylation User's Guide
- Working with DNAm data types
Download
Follow the installation instructions to use this package in your R session.
| Source package | recountmethylation_1.22.0.tar.gz |
| Windows binary (x86_64) | recountmethylation_1.22.0.zip |
| macOS binary (arm64) | recountmethylation_1.22.0.tgz |
| macOS binary (x86_64) | recountmethylation_1.22.0.tgz |
Dependencies
Depends: R (>= 4.1)
Imports: minfi, HDF5Array, rhdf5, S4Vectors, utils, methods, RCurl, R.utils, BiocFileCache, basilisk, reticulate, DelayedMatrixStats
Suggests: minfiData, minfiDataEPIC, knitr, testthat, ggplot2, gridExtra, rmarkdown, BiocStyle, GenomicRanges, limma, ExperimentHub, AnnotationHub