This package is considered a duplicate. The official version of this package is found at:https://hongxiang2023.r-universe.dev/MethScope

Package: MethScope 1.0.3

Hongxiang Fu

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.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://cran.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

zlib– Compression library

On CRAN:

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:6 OK. Indexed: no.

Target	Result	Time
linux-devel-arm64	OK	184
linux-devel-x86_64	OK	204
source / vignettes	OK	259
linux-release-arm64	OK	193
linux-release-x86_64	OK	219
wasm-release	OK	143

Exports:confidence_score confidence_score_top95 filter_cell GenerateInput GenerateReference imputeRowMean Input_training Liu2021_MouseBrain_P1000 nnls_deconv PlotConfusion PlotF1 PlotUMAP PlotUMAP_fixedwindow PredictCellType smooth_matrix Zhou2025_HumanAtlas_P1000

Dependencies:BH caret class cli clock codetools cpp11 data.table diagram digest doParallel dplyr dqrng e1071 farver FNN foreach future future.apply generics ggplot2 globals glue gower gtable hardhat ipred irlba isoband iterators jsonlite KernSmooth labeling lattice lava lifecycle listenv lubridate magrittr MASS Matrix ModelMetrics nlme nnet nnls numDeriv parallelly pillar pkgconfig plyr pROC prodlim progressr proxy purrr R6 RColorBrewer Rcpp RcppAnnoy RcppEigen RcppProgress recipes reshape2 rlang rpart RSpectra S7 scales shape sitmo sparsevctrs SQUAREM stringi stringr survival tibble tidyr tidyselect timechange timeDate tzdb utf8 uwot vctrs viridisLite withr xgboost

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

Help page	Topics
Produce confidence score for XGBoost prediction	confidence_score
Produce confidence score based on top 95 percent for XGBoost prediction	confidence_score_top95
Filter final prediction to reduce noise	filter_cell
Generate pattern level data for cell type annotation	GenerateInput
Generate reference pattern labels (no default writing)	GenerateReference
Impute missing value for 100K window matrix	imputeRowMean
Train XGBoost model to predict cell type	Input_training
Load the Liu et al. mouse brain pretrained model	Liu2021_MouseBrain_P1000
Estimate cell type relative proportion	nnls_deconv
Generate confusion table for the final prediction	PlotConfusion
Generate F1 score barplot for each class	PlotF1
Generate UMAP for the final prediction based on cell patterns	PlotUMAP
Generate UMAP for the final prediction based on fixed window eg.100kb bin widows	PlotUMAP_fixedwindow
Predict cell type annotation from the trained model	PredictCellType
Smooth cell by pattern matrix to reduce noise	smooth_matrix
Load the Zhou et al. human atlas pretrained model	Zhou2025_HumanAtlas_P1000

Package: MethScope 1.0.3

MethScope: Ultra-Fast Analysis of Sparse DNA Methylome via Recurrent Pattern Encoding

MethScope-MRMP

MethScope-Tutorial

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)