Ultra-Fast Analysis of Sparse DNA Methylome via Recurrent Pattern Encoding R package MethScope version 1.0.1 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. Software Depends: R (>= 2.10) Imports: xgboost, dplyr, utils, tidyr, stringr, caret, doParallel, parallel, ggplot2, uwot, magrittr, FNN, data.table, nnls Suggests: knitr, rmarkdown, spelling Hongxiang Fu <fhx@seas.upenn.edu> Comprehensive R Archive Network (CRAN) 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)) MIT + file LICENSE (https://CRAN.R-project.org/package=MethScope/LICENSE) 2026-02-26 application/tgz https://CRAN.R-project.org/package=MethScope doi:10.32614/CRAN.package.MethScope en-US