MethScope: Ultra-Fast Analysis of Sparse DNA Methylome via Recurrent Pattern Encoding
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.
| Version: | 1.0.0 |
| Depends: | R (≥ 2.10) |
| Imports: | xgboost, dplyr, utils, tidyr, stringr, caret, doParallel, parallel, ggplot2, uwot, magrittr, FNN, data.table, nnls |
| Suggests: | knitr, rmarkdown, spelling |
| Published: | 2025-12-09 |
| DOI: | 10.32614/CRAN.package.MethScope |
| Author: | Hongxiang Fu 
[aut, cre],
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 at seas.upenn.edu> |
| License: | MIT + file LICENSE |
| Copyright: | see file COPYRIGHTS |
| NeedsCompilation: | yes |
| Language: | en-US |
| Materials: | README |
| CRAN checks: | MethScope results |
Documentation:
| Reference manual: | MethScope.html , MethScope.pdf |
| Vignettes: |
MethScope-MRMP (source, R code) MethScope-Tutorial (source, R code) |
Downloads:
| Package source: | MethScope_1.0.0.tar.gz |
| Windows binaries: | r-devel: MethScope_1.0.0.zip, r-release: not available, r-oldrel: MethScope_1.0.0.zip |
| macOS binaries: | r-release (arm64): MethScope_1.0.0.tgz, r-oldrel (arm64): MethScope_1.0.0.tgz, r-release (x86_64): MethScope_1.0.0.tgz, r-oldrel (x86_64): MethScope_1.0.0.tgz |
Linking:
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