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R 040000
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.Rbuildignore 100644 0 kb
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DESCRIPTION 100644 2 kb
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bioc 100644 0 kb 100644 0 kb
[<img style="float: right;" src = "inst/figures/remeth_hexsticker.png" height="180"/>]( # Authors Sean K. Maden, Reid F. Thompson, Kasper D. Hansen, Abhinav Nellore # Overview The `recountmethylation` package provides access to databases of DNA methylation (DNAm) data from over 62,000 cumulative sample records with IDATs in the Gene Expression Omnibus (GEO, available by November, 2020). Samples were run using either of 2 Illumina BeadArray platform types, either the older HM450K platform or the newer EPIC/HM850K platform. The database compilation files include mined, mapped, and model-based sample metadata, and DNAm data in the form of either raw/unnormalized red and green signals, raw/unnormalized methylated and unmethylated signals, or normalized DNAm fractions (a.k.a. "Beta-values"). # Installation and data access From an active R session, install the latest available package version from Bioconductor with: ``` if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("recountmethylation") ``` You may also install the package from GitHub using: `require(devtools); install_github("metamaden/recountmethylation")`. See the package User's Guide vignette for more details and background about the datasets. # Manuscript If you use `recountmethylation` in published work, please cite the following paper: Sean K Maden and others, recountmethylation enables flexible analysis of public blood DNA methylation array data, Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad020, Sean K Maden, Reid F Thompson, Kasper D Hansen, Abhinav Nellore, 'Human methylome variation across Infinium 450K data on the Gene Expression Omnibus', NAR Genomics and Bioinformatics, Volume 3, Issue 2, June 2021, lqab025, Sean K Maden, # Package disclaimer Please note the following disclaimer regarding the data contained in the compilation files. ``` Databases accessed with recountmethylation contain data from GEO (, a live public database where alterations to online records can cause discrepancies with stored data over time. We cannot guarantee the accuracy of stored data, and advise users cross-check their findings with latest available records. ```