Package: MAGAR
Type: Package
Title: MAGAR: R-package to compute methylation Quantitative Trait Loci
        (methQTL) from DNA methylation and genotyping data
Version: 1.18.0
Date: 2024-11-13
Authors@R: c(
    person("Michael", "Scherer", email="michael.scherer@dkfz.de", role=c("cre", "aut"), comment = c(ORCID = "0000-0001-7990-6179"))
    )
Description: "Methylation-Aware Genotype Association in R" (MAGAR)
        computes methQTL from DNA methylation and genotyping data from
        matched samples. MAGAR uses a linear modeling stragety to call
        CpGs/SNPs that are methQTLs. MAGAR accounts for the local
        correlation structure of CpGs.
License: GPL-3
Imports: doParallel, igraph, bigstatsr, rjson, plyr, data.table,
        UpSetR, reshape2, jsonlite, methods, ff, argparse, impute,
        RnBeads.hg19, RnBeads.hg38, utils, stats
Depends: R (>= 4.1), HDF5Array, RnBeads, snpStats, crlmm
Suggests: gridExtra, VennDiagram, qqman, LOLA, RUnit, rmutil,
        rmarkdown, JASPAR2018, TFBSTools, seqLogo, knitr, devtools,
        BiocGenerics, BiocManager
Encoding: UTF-8
RoxygenNote: 7.2.3
VignetteBuilder: knitr
biocViews: Regression, Epigenetics, DNAMethylation, SNP,
        GeneticVariability, MethylationArray, Microarray, CpGIsland,
        MethylSeq, Sequencing, mRNAMicroarray, Preprocessing,
        CopyNumberVariation, TwoChannel, ImmunoOncology,
        DifferentialMethylation, BatchEffect, QualityControl,
        DataImport, Network, Clustering, GraphAndNetwork
BugReports: https://github.com/MPIIComputationalEpigenetics/MAGAR/issues
URL: https://github.com/MPIIComputationalEpigenetics/MAGAR
Config/pak/sysreqs: libglpk-dev make libbz2-dev libicu-dev liblzma-dev
        libpng-dev libxml2-dev libssl-dev python3 libx11-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:06:25 UTC
RemoteUrl: https://github.com/bioc/MAGAR
RemoteRef: RELEASE_3_22
RemoteSha: 07bf8e47af907ba6d7d5dddc2866ecc87f75a47d
NeedsCompilation: no
Packaged: 2025-11-11 21:12:31 UTC; root
Author: Michael Scherer [cre, aut] (ORCID:
    <https://orcid.org/0000-0001-7990-6179>)
Maintainer: Michael Scherer <michael.scherer@dkfz.de>
Built: R 4.5.2; ; 2025-11-12 03:23:35 UTC; windows
