CaDrA
Candidate Driver Analysis
Bioconductor version: 3.24 · Package version: 1.11.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Performs both stepwise and backward heuristic search for candidate (epi)genetic drivers based on a binary multi-omics dataset. CaDrA's main objective is to identify features which, together, are significantly skewed or enriched pertaining to a given vector of continuous scores (e.g. sample-specific scores representing a phenotypic readout of interest, such as protein expression, pathway activity, etc.), based on the union occurence (i.e. logical OR) of the events.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CaDrA")Details
| Maintainer | Reina Chau <rchau88@bu.edu> |
| Author | Reina Chau [aut, cre] (ORCID: <https://orcid.org/0000-0003-3012-1404>), Katia Bulekova [aut] (ORCID: <https://orcid.org/0000-0003-1560-2146>), Vinay Kartha [aut], Stefano Monti [aut] (ORCID: <https://orcid.org/0000-0002-9376-0660>) |
| License | GPL-3 + file LICENSE |
| URL | https://github.com/montilab/CaDrA/ |
| Bug Reports | https://github.com/montilab/CaDrA/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | FeatureExtraction, GeneExpression, Microarray, RNASeq, Software |
| Package Short Url | https://bioconductor.org/packages/CaDrA/ |
Citation
From within R, enter citation("CaDrA"):
Reina Chau, Katia Bulekova, Vinay Kartha, Stefano Monti. CaDrA: Candidate Driver Analysis. doi:10.18129/B9.bioc.CaDrA, R package version 1.11.0, https://bioconductor.org/packages/CaDrA.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | CaDrA_1.11.0.tar.gz |
| Windows binary (x86_64) | CaDrA_1.11.0.zip |
| macOS binary (arm64) | CaDrA_1.11.0.tgz |
| macOS binary (x86_64) | CaDrA_1.11.0.tgz |
Dependencies
Depends: R (>= 4.4.0)
Imports: doParallel, ggplot2, gplots, graphics, grid, gtable, knnmi, MASS, methods, misc3d, plyr, ppcor, R.cache, reshape2, stats, SummarizedExperiment
Suggests: BiocManager, devtools, knitr, pheatmap, rmarkdown, testthat (>= 3.1.6)