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CaDrA

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

Candidate Driver Analysis


Bioconductor version: Development (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 (from within R, enter citation("CaDrA")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("CaDrA")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF

Details

biocViews FeatureExtraction, GeneExpression, Microarray, RNASeq, Software
Version 1.1.2
In Bioconductor since BioC 3.18 (R-4.3) (< 6 months)
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)
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/CaDrA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CaDrA
Package Short Url https://bioconductor.org/packages/CaDrA/
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