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

0.1.1

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

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Benjamin Haibe-Kains2 releasesCRAN 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.

Install

BioconductorR (source archive)Ubuntu (r2u)

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.

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-coregx

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

CRAN check results are not tracked yet.

Code health

None

Tests · ratio 0.00

not tracked

Coverage

79%

Documentation · exports

Dependencies · direct

Documentation

READMENoVignettesNopkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 88%
Return-value docs: 80%
References docs: 5%

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on196 r2u732 bioconda

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.

Code & Tests

People & History

People (4)

Maintainer (1)

Benjamin Haibe-Kains

Author, Maintainer

Authors (4)

Author, Maintainer

Author

Author

Author

Package Timeline

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

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

Package metadata

Total releases: 2
License: GPL-3 OSI
Minimum R: ≥ 3.6.0
Bundled data: 2.6 MB / 2 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

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