R Observatory: Metrics for MethScope version 1.0.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MethScope

1.0.4Package record

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

0packages depend

2.8Kdownloads / year

3.0%test coverage

13/13flavors OK

Overview

About

Maintained by Hongxiang FuCRAN page ↗Declared funder: Wanding Zhou

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.

Changes in 1.0.4

Fixed Input_training(cross_validation = TRUE) with current xgboost releases by replacing the caret::train(method = "xgbTree") tuning path with native xgboost::xgb.cv() while preserving the MethScopeModel return structure used by PredictCellType().

From NEWS.md in the release

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("MethScope", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-methscope

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-MethScope

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-MethScope

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 4.2 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09

Show 6 earlier changesHide 6 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-02
ERROR11 OK, 1 ERROR2026-04-25
NOTE11 OK, 3 NOTE2026-04-10
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-09
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.4

READMEYes · 732 wordsVignettesYes · 6 · dynamicNEWSYes · 67% structured · mentions 1.0.4Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 16
Examples that run: 0%1 never run
Exported functions with examples: 6%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (6)

How these are measured

Downloads

2.8K

CRAN downloads in the past year

Rank #11,228 · ~8/day · ~236/mo

Releases R versions

Daily download trend is not available in this view yet.

33330 days

93390 days

2.8K1 year

Compare downloads with other packages →

Also on415 r2u6 autocran

How downloads are counted

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Installing MethScope adds 77 packages (45 with compiled code, 68 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB.

Depends (1)

R >= 4.0

Imports (14)

xgboost dplyrutilstidyr stringr caret doParallelparallelggplot2 uwot magrittr FNN data.table nnls

LinkingTo (0)

none

Suggests (4)

knitr rmarkdown spelling testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (4)

Hongxiang Fu

Author, Maintainer since 1.0.0 (2025)

The SAMtools/HTSlib authors

Contributor, Copyright holder

BGZF components; see inst/COPYRIGHTS

Attractive Chaos

Contributor, Copyright holder

Author and copyright holder of khash.h (klib, MIT license)

Wanding Zhou

Copyright holder, Funder

Releases (5)

Pick two releases to compare their code metrics.

1.0.4Latest
record
2026-08-26 · current release · diff ↗
1.0.3
record
2026-06-16 · diff ↗
1.0.2
record
2026-06-13 · diff ↗ ·
added 2 exports
Liu2021_MouseBrain_P1000, Zhou2025_HumanAtlas_P1000
R
R 4.6.0 released · 2026-04-24
1.0.1
record
2026-02-26 · diff ↗
1.0.0
record
2025-12-09
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-12-09
Total releases: 5 / 1 yrs
License: AGPL-3 OSI · relicensed from MIT + file LICENSE in 1.0.4
Minimum R: ≥ 4.0
Download size: 9.4 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("MethScope")

Format

Fu, H., The SAMtools/HTSlib authors, Chaos, A., & Zhou, W. (2026). MethScope: Ultra-Fast Analysis of Sparse DNA Methylome via Recurrent Pattern Encoding (Version 1.0.4) [Computer software]. https://doi.org/10.32614/CRAN.package.MethScope

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for MethScope version 1.0.4 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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