DOI: 10.18129/B9.bioc.CoreGx  

This is the development version of CoreGx; for the stable release version, see CoreGx.

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

Bioconductor version: Development (3.19)

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 'PharmacoSet' 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) . Manem, V., Labie, M., Smirnov, P., Kofia, V., Freeman, M., Koritzinksy, M., Abazeed, M., Haibe-Kains, B., Bratman, S. (2018) .

Author: Petr Smirnov [aut], Ian Smith [aut], Christopher Eeles [aut], Feifei Li [aut], Jermiah Joseph [aut], Benjamin Haibe-Kains [aut, cre]

Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains at>

Citation (from within R, enter citation("CoreGx")):


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biocViews Classification, Pharmacogenomics, Software, Survival
Version 2.7.0
In Bioconductor since BioC 3.11 (R-4.0) (3.5 years)
License GPL (>= 3)
Depends R (>= 4.1), BiocGenerics, SummarizedExperiment
Imports Biobase, S4Vectors, MultiAssayExperiment, MatrixGenerics, piano, BiocParallel, parallel, BumpyMatrix, checkmate, methods, stats, utils, graphics, grDevices, lsa, data.table, crayon, glue, rlang, bench
Suggests pander, markdown, BiocStyle, rmarkdown, knitr, formatR, testthat
Depends On Me PharmacoGx, RadioGx, ToxicoGx
Imports Me gDRimport, PDATK
Suggests Me
Links To Me
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