Package: ramwas
Type: Package
Title: Fast Methylome-Wide Association Study Pipeline for Enrichment
        Platforms
Version: 1.35.0
Date: 2019-02-18
Authors@R: c(person("Andrey A", "Shabalin",
                    role = c("aut", "cre"),
                    email = "andrey.shabalin@gmail.com",
                    comment = c(ORCID = "0000-0003-0309-6821")),
            person("Shaunna L", "Clark",
                    email = "slclark2@vcu.edu",
                    role = "aut"),
            person("Mohammad W", "Hattab",
                    email = "mwhattab@vcu.edu",
                    role = "aut"),
            person("Karolina A", "Aberg",
                    email = "kaaberg@vcu.edu",
                    role = "aut"),
            person("Edwin J C G", "van den Oord",
                    email = "ejvandenoord@vcu.edu",
                    role = "aut"))
Maintainer: Andrey A Shabalin <andrey.shabalin@gmail.com>
Description: A complete toolset for methylome-wide association studies
        (MWAS). It is specifically designed for data from enrichment
        based methylation assays, but can be applied to other data as
        well. The analysis pipeline includes seven steps: (1) scanning
        aligned reads from BAM files, (2) calculation of quality
        control measures, (3) creation of methylation score (coverage)
        matrix, (4) principal component analysis for capturing batch
        effects and detection of outliers, (5) association analysis
        with respect to phenotypes of interest while correcting for top
        PCs and known covariates, (6) annotation of significant
        findings, and (7) multi-marker analysis (methylation risk
        score) using elastic net. Additionally, RaMWAS include tools
        for joint analysis of methlyation and genotype data. This work
        is published in Bioinformatics, Shabalin et al. (2018)
        <doi:10.1093/bioinformatics/bty069>.
URL: https://bioconductor.org/packages/ramwas/
BugReports: https://github.com/andreyshabalin/ramwas/issues
License: LGPL-3
LazyLoad: yes
NeedsCompilation: yes
Depends: R (>= 3.3.0), methods, filematrix
VignetteBuilder: knitr
Suggests: knitr, rmarkdown, pander, BiocStyle,
        BSgenome.Ecoli.NCBI.20080805
Imports: graphics, stats, utils, digest, glmnet, KernSmooth, grDevices,
        GenomicAlignments, Rsamtools, parallel, biomaRt, Biostrings,
        BiocGenerics
biocViews: DNAMethylation, Sequencing, QualityControl, Coverage,
        Preprocessing, Normalization, BatchEffect, PrincipalComponent,
        DifferentialMethylation, Visualization
Config/pak/sysreqs: libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:36:00 UTC
RemoteUrl: https://github.com/bioc/ramwas
RemoteRef: HEAD
RemoteSha: 4c78862784c67b7db8bbb82fd52ae31fb5d2cae2
Packaged: 2026-02-21 07:50:56 UTC; root
Author: Andrey A Shabalin [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-0309-6821>),
  Shaunna L Clark [aut],
  Mohammad W Hattab [aut],
  Karolina A Aberg [aut],
  Edwin J C G van den Oord [aut]
Built: R 4.6.0; x86_64-apple-darwin20; 2026-02-21 07:54:55 UTC; unix
