CaDrA
Candidate Driver Analysis
Bioconductor version: Release (3.19)
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.
Author: Reina Chau [aut, cre] , Katia Bulekova [aut] , Vinay Kartha [aut], Stefano Monti [aut]
Maintainer: Reina Chau <rchau88 at bu.edu>
citation("CaDrA")
):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CaDrA")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CaDrA")
How to run CaDrA within a Docker Environment | HTML | |
Permutation-Based Testing | HTML | R Script |
Scoring Functions | HTML | R Script |
Reference Manual | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | FeatureExtraction, GeneExpression, Microarray, RNASeq, Software |
Version | 1.2.0 |
In Bioconductor since | BioC 3.18 (R-4.3) (1 year) |
License | GPL-3 + file LICENSE |
Depends | R (>= 4.3.0) |
Imports | doParallel, ggplot2, gplots, graphics, grid, gtable, MASS, methods, misc3d, plyr, ppcor, R.cache, reshape2, stats, SummarizedExperiment |
System Requirements | |
URL | https://github.com/montilab/CaDrA/ |
Bug Reports | https://github.com/montilab/CaDrA/issues |
See More
Suggests | BiocManager, devtools, knitr, pheatmap, rmarkdown, testthat (>= 3.1.6) |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | CaDrA_1.2.0.tar.gz |
Windows Binary | CaDrA_1.2.0.zip (64-bit only) |
macOS Binary (x86_64) | CaDrA_1.2.0.tgz |
macOS Binary (arm64) | CaDrA_1.2.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/CaDrA |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CaDrA |
Bioc Package Browser | https://code.bioconductor.org/browse/CaDrA/ |
Package Short Url | https://bioconductor.org/packages/CaDrA/ |
Package Downloads Report | Download Stats |