Package: MethScope 1.0.3

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.

Authors:Hongxiang Fu [aut, cre], Wanding Zhou [cph, fnd], The SAMtools/HTSlib authors [ctb, cph], Attractive Chaos [ctb, cph]

MethScope_1.0.3.tar.gz
MethScope_1.0.3.zip(r-4.7)MethScope_1.0.3.zip(r-4.6)MethScope_1.0.3.zip(r-4.5)
MethScope_1.0.3.tgz(r-4.6-x86_64)MethScope_1.0.3.tgz(r-4.6-arm64)MethScope_1.0.3.tgz(r-4.5-x86_64)MethScope_1.0.3.tgz(r-4.5-arm64)
MethScope_1.0.3.tar.gz(r-4.7-arm64)MethScope_1.0.3.tar.gz(r-4.7-x86_64)MethScope_1.0.3.tar.gz(r-4.6-arm64)MethScope_1.0.3.tar.gz(r-4.6-x86_64)
MethScope_1.0.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
MethScope/json (API)

# Install 'MethScope' in R:
install.packages('MethScope', repos = c('https://hongxiang2023.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • zlib– Compression library

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

zlib

3.60 score 8 scripts 264 downloads 16 exports 87 dependencies

Last updated from:a19490d358. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK185
linux-devel-x86_64OK252
source / vignettesOK244
linux-release-arm64OK233
linux-release-x86_64OK204
macos-release-arm64OK163
macos-release-x86_64OK352
macos-oldrel-arm64OK105
macos-oldrel-x86_64OK307
windows-develOK165
windows-releaseOK156
windows-oldrelOK150
wasm-releaseOK145

Exports:confidence_scoreconfidence_score_top95filter_cellGenerateInputGenerateReferenceimputeRowMeanInput_trainingLiu2021_MouseBrain_P1000nnls_deconvPlotConfusionPlotF1PlotUMAPPlotUMAP_fixedwindowPredictCellTypesmooth_matrixZhou2025_HumanAtlas_P1000

Dependencies:BHcaretclasscliclockcodetoolscpp11data.tablediagramdigestdoParalleldplyrdqrnge1071farverFNNforeachfuturefuture.applygenericsggplot2globalsgluegowergtablehardhatipredirlbaisobanditeratorsjsonliteKernSmoothlabelinglatticelavalifecyclelistenvlubridatemagrittrMASSMatrixModelMetricsnlmennetnnlsnumDerivparallellypillarpkgconfigplyrpROCprodlimprogressrproxypurrrR6RColorBrewerRcppRcppAnnoyRcppEigenRcppProgressrecipesreshape2rlangrpartRSpectraS7scalesshapesitmosparsevctrsSQUAREMstringistringrsurvivaltibbletidyrtidyselecttimechangetimeDatetzdbutf8uwotvctrsviridisLitewithrxgboost

MethScope-MRMP

Rendered fromMethScope-MRMP.Rmdusingknitr::rmarkdownon Jun 16 2026.

Last update: 2025-12-09
Started: 2025-12-09

MethScope-Tutorial

Rendered fromMethScope-Tutorial.Rmdusingknitr::rmarkdownon Jun 16 2026.

Last update: 2026-06-16
Started: 2025-12-09