R Observatory: Metrics for oncoPredict version 1.3.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

oncoPredict

1.3.1

Drug Response Modeling and Biomarker Discovery

0packages depend

2.5Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Robert GruenerFirst published 2026-06-294 releasesCRAN page ↗GitHub ↗

Allows for building drug response models using screening data between bulk RNA-Seq and a drug response metric and two additional tools for biomarker discovery that have been developed by the Huang Laboratory at University of Minnesota. There are 3 main functions within this package. (1) calcPhenotype() is used to build drug response models on RNA-Seq data and impute them on any other RNA-Seq dataset given to the model. (2) GLDS() is used to calculate the general level of drug sensitivity, which can improve biomarker discovery. (3) IDWAS() can take the results from calcPhenotype() and link the imputed response back to available genomic (mutation and CNV alterations) to identify biomarkers. Each of these functions comes from a paper from the Huang research laboratory. Below gives the relevant paper for each function. The package is described in Maeser et al. (2021) "oncoPredict: an R package for predicting in vivo or cancer patient drug response and biomarkers from cell line screening data" doi:10.1093/bib/bbab260. calcPhenotype() - Geeleher et al, Clinical drug response can be predicted using baseline gene expression levels and in vitro drug sensitivity in cell lines. GLDS() - Geeleher et al, Cancer biomarker discovery is improved by accounting for variability in general levels of drug sensitivity in pre-clinical models. IDWAS() - Geeleher et al, Discovering novel pharmacogenomic biomarkers by imputing drug response in cancer patients from large genomics studies.

Install

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

install.packages("oncoPredict", 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("HuangLabUMN/oncoPredict")

Development version from HuangLabUMN/oncoPredict. 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-oncopredict

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

13OK

Slowest check: 12.4 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.20

not tracked

Coverage

100%

Documentation · exports

12

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
OK2026-06-30
7 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 413 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

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

Downloads

2.5K

CRAN downloads in the past year

Rank #3,760 · ~7/day · ~210/mo

Releases R versions

Daily download trend is not available in this view yet.

1.4K30 days

2.4K90 days

2.5K1 year

Compare downloads with other packages →

Also on100 r2u

Repository

GitHub ↗ huanglabumn/oncopredict

35Stars

5Forks

3Open issues

0Open PRs

0Releases

32Commits

2Contributors

32 commits · Last activity 2026-06-13 · +9.4% stars, 30d

Stars over time

2025-08-14 · 202026-08-13 · 35

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/huanglabumn/oncopredict on 2026-08-16.

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (12)

parallelridge car glmnet pls sva limma GenomicFeatures BiocGenerics GenomicRanges IRanges S4Vectors

LinkingTo (0)

none

Suggests (6)

knitr rmarkdown org.Hs.eg.db TxDb.Hsapiens.UCSC.hg19.knownGene TCGAbiolinks testthat (>= 3.0.0)

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Robert Gruener

Author, Maintainer

Authors (2)

Robert Gruener

Author, Maintainer

Danielle Maeser

Author

Package Timeline

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

1.3.1Latest
2026-06-29 · current release · diff ↗
unarchivedReturned to CRAN
2026-06-29
R
R 4.6.0 released · 2026-04-24
archivedRemoved from CRAN
2025-10-23
check issues were not corrected in time
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.2
2024-04-05 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.2
2021-09-24 · diff ↗
unarchivedReturned to CRAN
2021-09-24
archivedRemoved from CRAN
2021-09-18
policy violation on Internet access
0.1
2021-06-04
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2026-06-29
Total releases: 4 / 1 yrs
License: GPL-2 OSI
Additional repositories: bioconductor.org
Minimum R: ≥ 4.1.0
Download size: 2.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("oncoPredict")

Format

Gruener, R., & Maeser, D. (2026). oncoPredict: Drug Response Modeling and Biomarker Discovery (Version 1.3.1) [Computer software]. https://doi.org/10.32614/CRAN.package.oncoPredict

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 oncoPredict version 1.3.1 [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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