R Observatory: Metrics for MethScope version 1.0.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MethScope

1.0.3

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

0packages depend

2.1Kdownloads / year

3.0%test coverage

13/13checks pass

Overview

About

Maintained by Hongxiang FuFirst published 2025-12-094 releasesCRAN page ↗

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.

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.

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).

Health

CRAN checks

13OK

Slowest check: 4.2 min · r-release-macos-x86_64

Code health

Yes

Tests · ratio 0.09

3.0%

Coverage · measured lines

100%

Documentation · exports

14

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 4 earlier snapshots

ERROR2026-04-25
11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 186 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 67%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

2.1K

CRAN downloads in the past year

Rank #12,360 · ~6/day · ~174/mo

Releases R versions

Daily download trend is not available in this view yet.

19430 days

80690 days

2.1K1 year

Compare downloads with other packages →

Also on363 r2u

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

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.

Code & Tests

People & History

People (4)

Maintainer (1)

Hongxiang Fu

Author, Maintainer

Authors (1)

Hongxiang Fu

Author, Maintainer

Contributors (2)

The SAMtools/HTSlib authors

Contributor, Copyright holder

Attractive Chaos

Contributor, Copyright holder

Copyright holders (3)

The SAMtools/HTSlib authors

Contributor, Copyright holder

Attractive Chaos

Contributor, Copyright holder

Wanding Zhou

Copyright holder, Funder

Funders (1)

Wanding Zhou

Copyright holder, Funder

Package Timeline

4 releases. Pick two to compare their code metrics. R releases are shown for context.

1.0.3Latest
2026-06-16 · current release · diff ↗
1.0.2
2026-06-13 · diff ↗
R
R 4.6.0 released · 2026-04-24
1.0.1
2026-02-26 · diff ↗
1.0.0
2025-12-09
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-12-09
Total releases: 4 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.0
Download size: 7.1 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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 1.0.3) [Computer software]. https://doi.org/10.32614/CRAN.package.MethScope

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 1.0.3 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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