Package: MethScope
Title: Ultra-Fast Analysis of Sparse DNA Methylome via Recurrent
        Pattern Encoding
Version: 1.0.3
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: MIT + file LICENSE
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
Packaged: 2026-06-15 19:21:23 UTC; fuh1
Maintainer: Hongxiang Fu <fhx@seas.upenn.edu>
Language: en-US
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))
Repository: CRAN
Date/Publication: 2026-06-16 07:00:16 UTC
Built: R 4.6.1; x86_64-w64-mingw32; 2026-07-28 05:36:13 UTC; windows
Archs: x64
