mmcmcBayes

0.2.0

Multistage MCMC Method for Detecting DMRs

0packages depend

3.5Kdownloads / year

–test coverage

12/13checks pass

Overview

About

Maintained by Zhexuan YangFirst published 2025-11-242 releasesCRAN page ↗GitHub ↗

Implements differential methylation region (DMR) detection using a multistage Markov chain Monte Carlo (MCMC) algorithm based on the alpha-skew generalized normal (ASGN) distribution. Version 0.2.0 removes the Anderson-Darling test stage, improves computational efficiency of the core ASGN and multistage MCMC routines, and adds convenience functions for summarizing and visualizing detected DMRs. The methodology is based on Yang (2025) https://www.proquest.com/docview/3218878972.

Install

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

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

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

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("zyang1919/mmcmcBayes")

Development version from zyang1919/mmcmcBayes. Installs pak first if it is not already available.

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-mmcmcbayes

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-mmcmcBayes

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-mmcmcBayes

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 2.1 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-08
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-06-07
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 29%
Documented parameters: 91%
Return-value docs: 100%
References docs: 14%

Downloads

3.5K

CRAN downloads in the past year

Rank #9,599 · ~10/day · ~289/mo

Releases R versions

Daily download trend is not available in this view yet.

20330 days

1.1K90 days

3.5K1 year

Compare downloads with other packages →

Also on111 r2u

Repository

GitHub ↗ zyang1919/mmcmcbayes

0Stars

0Forks

0Open issues

0Open PRs

0Releases

Last activity 2025-12-26

Repository practices

Upstream repositoryBeta

Checks run against github.com/zyang1919/mmcmcbayes on 2026-07-31.

No development-tooling practices detected in the upstream repository.

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0.0

Imports (3)

statsgraphicsMCMCpack

LinkingTo (0)

none

Suggests (4)

kSamples testthat knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Zhexuan Yang

Author, Maintainer

Authors (3)

Zhexuan Yang

Author, Maintainer

Feng Luan

Author

Duchwan Ryu

Author

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.2.0Latest
2025-12-21 · current release · diff ↗
0.1.0
2025-11-24
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-11-24
Total releases: 2 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.0.0
Bundled data: 6.0 MB / 2 files
Download size: 6.0 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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