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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.
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Package details |
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| 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> |
| License | MIT + file LICENSE |
| Version | 1.0.1 |
| Package repository | View on CRAN |
| Installation |
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