Package: methylTFR
Title: Quantification of DNA Methylation Signatures in TFBS
Version: 0.99.9
Date: 2026-09-29
Authors@R: c(
    person("Irem B.", "Gündüz", , "irembgunduz@gmail.com", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0003-2641-0916")),
    person("Sarath Kumar", "Murugan", , "sarath.murugan@outlook.com", role = "aut",
           comment = c(ORCID = "0000-0001-7378-7869")),
    person("Fabian", "Mueller", , "fabian.mueller@uni-saarland.de", role = "aut",
           comment = c(ORCID = "0000-0001-5809-2321")),
    person("ERA-NET Transcan-Neu III - EPILUNAR", role = "fnd",
           comment = "Grant 01KT2409"),
    person("Saarland University", role = "fnd",
           comment = "NanoBioMed Young Investigator Grant")
  )
Description: methylTFR is an extensive R package designed specifically
        for analyzing DNA methylation signatures within transcription
        factor binding sites (TFBS) across diverse genomic annotations.
        It enhances methylation analysis by calculating a
        bias-corrected 'deviation' in methylation levels, leveraging GC
        bias distribution and frequency data.  This package offers a
        variety of functions that facilitate the motif activity
        exhibiting diverse methylation patterns across distinct samples
        or cells.
License: MIT + file LICENSE
URL: https://github.com/EpigenomeInformatics/methylTFR,
        https://epigenomeinformatics.github.io/methylTFR/
BugReports: https://support.bioconductor.org/t/methylTFR
Depends: data.table (>= 1.14.0), R (>= 4.3.0), SummarizedExperiment
Imports: BiocGenerics, BiocParallel, DelayedArray, GenomicRanges,
        ggplot2, HDF5Array, IRanges, logger, matrixStats, methods,
        R.utils, S4Vectors, stats, stringr, utils
Suggests: BiocStyle, circlize, ComplexHeatmap, grid, knitr, RefManageR,
        RnBeads, RnBeads.hg38, rmarkdown, sessioninfo, testthat (>=
        3.0.0)
VignetteBuilder: knitr
biocViews: Software, DNAMethylation, SingleCell, StatisticalMethod,
        GeneRegulation, Epigenetics,Transcription, Sequencing,
        WholeGenome, DifferentialMethylation, MotifAnnotation,
        MotifDiscovery, Coverage
Config/testthat/edition: 3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Config/pak/sysreqs: libicu-dev libssl-dev zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-09-29 14:47:24 UTC
RemoteUrl: https://github.com/BiocStaging/methylTFR
RemoteRef: HEAD
RemoteSha: 22b85e97f96ec40c9110ce35c73c1402542404ff
NeedsCompilation: no
Packaged: 2026-09-29 16:13:34 UTC; root
Author: Irem B. Gündüz [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-2641-0916>),
  Sarath Kumar Murugan [aut] (ORCID:
    <https://orcid.org/0000-0001-7378-7869>),
  Fabian Mueller [aut] (ORCID: <https://orcid.org/0000-0001-5809-2321>),
  ERA-NET Transcan-Neu III - EPILUNAR [fnd] (Grant 01KT2409),
  Saarland University [fnd] (NanoBioMed Young Investigator Grant)
Maintainer: Irem B. Gündüz <irembgunduz@gmail.com>