Package: MethScope
Title: Ultra-Fast Analysis of Sparse DNA Methylome via Recurrent
        Pattern Encoding
Version: 1.0.4
Authors@R: c(
    person("Hongxiang", "Fu", , "fhx@seas.upenn.edu", role = c("aut", "cre"),comment = c(ORCID = "0000-0002-9873-8606")),
    person("Wanding", "Zhou", , "wanding.zhou@pennmedicine.upenn.edu", role = c("cph", "fnd")),
    person("The SAMtools/HTSlib authors", role = c("ctb","cph"),
         comment = "BGZF components; see inst/COPYRIGHTS"),
    person(given = "Attractive", family = "Chaos",
         role = c("ctb","cph"),
         comment = "Author and copyright holder of khash.h (klib, MIT license)")
    )
Description: Methods for analyzing DNA methylation data via Most
        Recurrent Methylation Patterns (MRMPs). Supports cell-type
        annotation, spatial deconvolution, unsupervised clustering, and
        cancer cell-of-origin inference. Includes C-backed summaries
        for YAME ".cg/.cm" files (overlap counts, log2 odds ratios,
        beta/depth aggregation), an XGBoost classifier, NNLS
        deconvolution, and plotting utilities. Scales to large spatial
        and single-cell methylomes and is robust to extreme sparsity.
License: AGPL-3
Encoding: UTF-8
RoxygenNote: 7.3.2
Imports: xgboost, dplyr, utils, tidyr, stringr, caret, doParallel,
        parallel, ggplot2, uwot, magrittr, FNN, data.table, nnls
Suggests: knitr, rmarkdown, spelling, testthat
VignetteBuilder: knitr
Depends: R (>= 4.0)
SystemRequirements: zlib
NeedsCompilation: yes
Language: en-US
Packaged: 2026-09-26 06:34:27 UTC; root
Author: Hongxiang Fu [aut, cre] (ORCID:
        <https://orcid.org/0000-0002-9873-8606>), Wanding Zhou [cph,
        fnd], The SAMtools/HTSlib authors [ctb, cph] (BGZF components;
        see inst/COPYRIGHTS), Attractive Chaos [ctb, cph] (Author and
        copyright holder of khash.h (klib, MIT license))
Maintainer: Hongxiang Fu <fhx@seas.upenn.edu>
Config/pak/sysreqs: make libicu-dev zlib1g-dev
Repository: https://hongxiang2023.r-universe.dev
Date/Publication: 2026-08-26 23:46:18 UTC
RemoteUrl: https://github.com/cran/MethScope
RemoteRef: HEAD
RemoteSha: e927782e5dbbbf4a3a895ba6ba114d88bae648d8