MethScope: Ultra-Fast Analysis of Sparse DNA Methylome via RecurrentPattern 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 + fileLICENSE |
| Copyright: | see fileCOPYRIGHTS |
| 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:MethScope_1.0.0.zip, 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:
Please use the canonical formhttps://CRAN.R-project.org/package=MethScopeto link to this page.