Package: dmsa
Title: Directional Methylation Set Analysis
Version: 0.99.11
Authors@R: c(person("Tsachi", "Ein-Dor", role = c("aut", "cre", "fnd"),
    email = "teindor@runi.ac.il",
    comment = c(ORCID = "0000-0002-3078-7591")))
URL: https://github.com/teindor/dmsa, https://teindor.github.io/dmsa
BugReports: https://github.com/teindor/dmsa/issues
Description: Aligns probe-level methylation effects to their predicted
        effect on gene expression and, for system-level analysis, to
        each gene's curated polarity with respect to the system's
        activation tone (e.g. NR3C1 opposes HPA-axis activation). Pools
        the aligned coefficients with fixed-sign or expected-sign
        estimators and reports coverage and activation/brake balance
        per set. Ships the Project Alpha gene-system map, a
        gene-to-system polarity table carrying a stated source and
        review flag on every row, and a curated system > module > gene
        > probe selection cascade whose module labels carry
        literature-audited evidence tiers and citations; genes without
        a polarity entry must be specified by the user.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.5.0)
Imports: stats, utils, methods, grDevices, graphics, data.table,
        SummarizedExperiment
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, gt, lme4, lmerTest,
        MASS, nnet, viridisLite, beepr, png, Gviz, GenomicRanges,
        IRanges, GenomicFeatures, ensembldb, AnnotationDbi,
        AnnotationFilter
biocViews: DNAMethylation, DifferentialMethylation, MethylationArray,
        GeneSetEnrichment, GeneExpression, Epigenetics, Microarray,
        Coverage, StatisticalMethod, MultipleComparison, Regression,
        Software
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-09-03 07:28:54 UTC
RemoteUrl: https://github.com/BiocStaging/dmsa
RemoteRef: HEAD
RemoteSha: 958def1e80f29396dba951b9de03d547f9f22935
NeedsCompilation: no
Packaged: 2026-10-08 12:44:45 UTC; root
Author: Tsachi Ein-Dor [aut, cre, fnd] (ORCID:
    <https://orcid.org/0000-0002-3078-7591>)
Maintainer: Tsachi Ein-Dor <teindor@runi.ac.il>