oncoPredict: Drug Response Modeling and Biomarker Discovery

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. 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.

Version: 1.2
Depends: R (≥ 4.1.0)
Imports: parallel, ridge, car, glmnet, pls, sva, preprocessCore, GenomicFeatures, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, tidyverse, TCGAbiolinks, BiocGenerics, GenomicRanges, IRanges, S4Vectors
Suggests: knitr, rmarkdown, gdata, genefilter, maftools, readxl, testthat (≥ 3.0.0)
Published: 2024-04-05
Author: Danielle Maeser ORCID iD [aut], Robert Gruener [aut, cre]
Maintainer: Robert Gruener <rgruener at umn.edu>
BugReports: https://github.com/HuangLabUMN/oncoPredict/issues
License: GPL-2
URL: https://github.com/HuangLabUMN/oncoPredict
NeedsCompilation: no
Materials: README
In views: Omics
CRAN checks: oncoPredict results

Documentation:

Reference manual: oncoPredict.pdf
Vignettes: calcPhenotype
cnv
glds
mut

Downloads:

Package source: oncoPredict_1.2.tar.gz
Windows binaries: r-devel: oncoPredict_1.2.zip, r-release: oncoPredict_1.2.zip, r-oldrel: oncoPredict_1.2.zip
macOS binaries: r-release (arm64): oncoPredict_0.2.tgz, r-oldrel (arm64): oncoPredict_1.2.tgz, r-release (x86_64): oncoPredict_0.2.tgz
Old sources: oncoPredict archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=oncoPredict to link to this page.