R Observatory: Metrics for CoreGx version 0.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2020-03-29. Its history is shown below.

Reason: requested by the maintainer

Details below reflect version 0.1.1, its last release before removal.

CoreGx

0.1.1Package record

Classes and Functions to Serve as the Basis for Other 'Gx' Packages

0packages depend

–downloads / year

–test coverage

–flavors OK

Overview

About

Maintained by Benjamin Haibe-KainsCRAN page ↗

A collection of functions and classes which serve as the foundation for our lab's suite of R packages, such as 'PharmacoGx' and 'RadioGx'. This package was created to abstract shared functionality from other lab package releases to increase ease of maintainability and reduce code repetition in current and future 'Gx' suite programs. Major features include a 'CoreSet' class, from which 'RadioSet' and 'PharmaSet' are derived, along with get and set methods for each respective slot. Additional functions related to fitting and plotting dose response curves, quantifying statistical correlation and calculating area under the curve (AUC) or survival fraction (SF) are included. For more details please see the included documentation, as well as: Smirnov, P., Safikhani, Z., El-Hachem, N., Wang, D., She, A., Olsen, C., Freeman, M., Selby, H., Gendoo, D., Grossman, P., Beck, A., Aerts, H., Lupien, M., Goldenberg, A. (2015) doi:10.1093/bioinformatics/btv723. Manem, V., Labie, M., Smirnov, P., Kofia, V., Freeman, M., Koritzinksy, M., Abazeed, M., Haibe-Kains, B., Bratman, S. (2018) doi:10.1101/449793.

Changes in 0.1.1

Bug Fixes

Changed class(x) == 'matrix' to is.matrix(x) to prevent breaking backwards compatibility for R-devel.

From NEWS.md in the release

Install

BioconductorR (source archive)

BiocManager::install("CoreGx")

Installs the current Bioconductor release. Requires the BiocManager package.

url <- "https://cran.r-project.org/src/contrib/Archive/CoreGx/CoreGx_0.1.1.tar.gz"
pkgFile <- "CoreGx_0.1.1.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (0.1.1) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

Health

CRAN checks

CRAN check results are not tracked yet.

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.1

READMENoVignettesNoNEWSYes · 67% structured · mentions 0.1.1Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 41
Examples that run: 100%37 run in a plain check
Exported functions with examples: 87%
Documented parameters: 88%
Return-value docs: 80%
Help pages citing references: 5%

How these are measured

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on260 r2u941 bioconda

How downloads are counted

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.6.0

Imports (6)

lsamethodspiano Biobasestatsrlang

LinkingTo (0)

none

Suggests (1)

PharmacoGx

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (4)

Benjamin Haibe-Kains

Author, Maintainer since 0.1.0 (2019)

Petr Smirnov

Author

Ian Smith

Author

Christopher Eeles

Author

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.0.0 released · 2020-04-24
archivedRemoved from CRAN
2020-03-29
requested by the maintainer
0.1.1
record
2019-12-19 · diff ↗
0.1.0
record
2019-06-14
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-06-14
Total releases: 2 / 7 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.6.0
Bundled data: 2.6 MB / 2 files

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("CoreGx")

Format

Smirnov, P., Smith, I., Eeles, C., & Haibe-Kains, B. (n.d.). CoreGx: Classes and Functions to Serve as the Basis for Other 'Gx' Packages (Version 0.1.1) [Computer software]. Retrieved October 23, 2026, from https://CRAN.R-project.org/package=CoreGx

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 CoreGx version 0.1.1 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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