R Observatory: Metrics for MBMethPred version 0.1.4.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MBMethPred

0.1.4.4

Medulloblastoma Subgroups Prediction

0packages depend

3Kdownloads / year

63.4%test coverage

11/13checks pass

Overview

About

Maintained by Edris Sharif RahmaniFirst published 2022-12-137 releasesCRAN page ↗GitHub ↗

Utilizing a combination of machine learning models (Random Forest, Naive Bayes, K-Nearest Neighbor, Support Vector Machines, Extreme Gradient Boosting, and Linear Discriminant Analysis) and a deep Artificial Neural Network model, 'MBMethPred' can predict medulloblastoma subgroups, including wingless (WNT), sonic hedgehog (SHH), Group 3, and Group 4 from DNA methylation beta values. See Sharif Rahmani E, Lawarde A, Lingasamy P, Moreno SV, Salumets A and Modhukur V (2023), MBMethPred: a computational framework for the accurate classification of childhood medulloblastoma subgroups using data integration and AI-based approaches. Front. Genet. 14:1233657. <doi: 10.3389/fgene.2023.1233657> for more details.

Install

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

install.packages("MBMethPred", 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("sharifrahmanie/MBMethPred")

Development version from sharifrahmanie/MBMethPred. 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-mbmethpred

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-MBMethPred

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-MBMethPred

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

Health

CRAN checks

2NOTE11OK

Failing flavors

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

Slowest check: 5.4 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 0.07

63.4%

Coverage · measured lines

100%

Documentation · exports

20

Dependencies · direct

Check history

NOTE2026-07-11
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
ERROR2026-04-25
11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,225 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 79%
Documented parameters: 100%
Return-value docs: 100%
References docs: 16%

Downloads

3K

CRAN downloads in the past year

Rank #15,928 · ~8/day · ~251/mo

Releases R versions

Daily download trend is not available in this view yet.

14430 days

66090 days

3K1 year

Compare downloads with other packages →

Also on243 r2u19 autocran

Repository

GitHub ↗ sharifrahmanie/mbmethpred

0Stars

0Forks

0Open issues

0Open PRs

1Releases

38Commits

2Contributors

38 commits · Last activity 2025-12-04

Repository practices

Upstream repositoryBeta

Checks run against github.com/sharifrahmanie/mbmethpred on 2026-08-16.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

21 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (20)

stringr ggplot2parallelcaTools caret kerasMASSRtsne SNFtoolclassdplyr e1071 pROC randomForest readr reshape2 reticulate rgl tensorflow xgboost

LinkingTo (0)

none

Suggests (6)

knitr rmarkdown testthatutilsstatsscales

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Edris Sharif Rahmani

Author, Contributor, Maintainer

Authors (3)

Edris Sharif Rahmani

Author, Contributor, Maintainer

Vijayachitra Modhukur

Author, Contributor

Ankita Sunil Lawarde

Author, Contributor

Contributors (3)

Edris Sharif Rahmani

Author, Contributor, Maintainer

Vijayachitra Modhukur

Author, Contributor

Ankita Sunil Lawarde

Author, Contributor

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.1.4.4Latest
2025-12-04 · current release · diff ↗
0.1.4.3
2025-06-17 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.1.4.2
2023-09-18 · diff ↗
0.1.4
2023-07-11 · diff ↗
0.1.2
2023-07-03 · diff ↗
0.1.1
2023-07-01 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.1.0
2022-12-13
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-12-13
Total releases: 7 / 4 yrs
License: GPL
Minimum R: ≥ 3.5.0
Bundled data: 2.9 MB / 4 files
Download size: 3.0 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("MBMethPred")

Format

Sharif Rahmani, E., Modhukur, V., & Sunil Lawarde, A. (2025). MBMethPred: Medulloblastoma Subgroups Prediction (Version 0.1.4.4) [Computer software]. https://doi.org/10.32614/CRAN.package.MBMethPred

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 MBMethPred version 0.1.4.4 [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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