Package: cpgdirection
Type: Package
Title: Predict the Direction of CpG-Gene Expression Associations
Version: 2.99.5
Authors@R: c(
 person("Tsachi", "Ein-Dor", email = "teindor@runi.ac.il",
 role = c("aut", "cre", "fnd"),
 comment = c(ORCID = "0000-0002-3078-7591")))
Description: Assigns a direction to the association between DNA
        methylation at a CpG site and the expression of a nearby gene,
        for CpGs that have no measured expression quantitative trait
        methylation (eQTM) record. Predictions come from a precomputed
        table of 3,105,697 CpG-gene pairs covering 761,445 CpGs,
        assembled from four sources of evidence: directly measured
        eQTMs, summary-data Mendelian randomisation using genetic
        instruments, gradient-boosted models of genomic context and
        local catalogue structure fitted separately in blood, nasal
        epithelium and solid tissue, and a distance prior. Each call
        returns a direction, a calibrated probability, an evidence tier
        and an expected accuracy, and abstains where the evidence is
        insufficient. Predictions estimate direction conditional on the
        CpG being an eQTM; they do not establish that an effect exists.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.5.0)
Imports: data.table (>= 1.14.0), utils, stats,
        TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db,
        GenomicFeatures, GenomicRanges, AnnotationDbi, cpgdirectionData
Suggests: testthat (>= 3.0.0), gt (>= 0.9.0), knitr, rmarkdown
VignetteBuilder: knitr
biocViews: DNAMethylation, GeneExpression, GeneRegulation, GeneTarget,
        Epigenetics, Annotation
URL: https://github.com/teindor/cpgdirection,
        https://doi.org/10.17605/OSF.IO/U3VFK
BugReports: https://github.com/teindor/cpgdirection/issues
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-09-02 14:15:15 UTC
RemoteUrl: https://github.com/BiocStaging/cpgdirection
RemoteRef: HEAD
RemoteSha: 3e1d93c7a91503cf949dbd3fac28c60f474b2900
NeedsCompilation: no
Packaged: 2026-10-10 15:18:23 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>