Package: MAGAR
Type: Package
Title: MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data
Version: 1.19.0
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
git_url: https://git.bioconductor.org/packages/MAGAR
git_branch: devel
git_last_commit: ac78c53
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
