R Observatory: Metrics for OncoSubtype version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

OncoSubtype

1.0.0

Predict Cancer Subtypes Based on TCGA Data using Machine Learning Method

0packages depend

2.3Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Dadong ZhangFirst published 2024-03-221 releasesCRAN page ↗GitHub ↗

Provide functionality for cancer subtyping using nearest centroids or machine learning methods based on TCGA data.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("OncoSubtype", 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("DadongZ/OncoSubtype")

Development version from DadongZ/OncoSubtype. 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-oncosubtype

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

Health

CRAN checks

2NOTE11OK

Failing flavors

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

Slowest check: 8.7 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.03

not tracked

Coverage

100%

Documentation · exports

11

Dependencies · direct

Check history

NOTE2026-06-09
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
11 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-05-10
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-03
10 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-05-02
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 4 earlier snapshots

ERROR2026-04-25
9 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-03
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-02
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 208 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 94%
Return-value docs: 100%
References docs: 8%

Downloads

2.3K

CRAN downloads in the past year

Rank #14,608 · ~6/day · ~192/mo

Releases R versions

Daily download trend is not available in this view yet.

20730 days

70990 days

2.3K1 year

Compare downloads with other packages →

Also on125 r2u

Repository

GitHub ↗ dadongz/oncosubtype

1Stars

1Forks

0Open issues

1Open PRs

0Releases

10Commits

2Contributors

10 commits · Last activity 2025-05-16

Stars over time

2024-12-06 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/dadongz/oncosubtype on 2026-08-16.

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.63SummarizedExperiment

Imports (10)

caret randomForestmethodse1071 pheatmap tibble dplyr limma rlang Rdpack

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (0)

Author records are not tracked yet for this package.

Listed in earlier versions (1)

Dadong Zhang

no longer listed · 1.0.0

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2024-03-22
Total releases: 1 / 2 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.63
Bundled data: 1.3 MB / 4 files
Download size: 1.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("OncoSubtype")

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 OncoSubtype version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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