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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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("CaDrA")
Permutation-Based Testing HTML R Script
Scoring Functions HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews FeatureExtraction, GeneExpression, Microarray, RNASeq, Software
Version 1.1.1
In Bioconductor since BioC 3.18 (R-4.3) (< 6 months)
License GPL-3 + file LICENSE
Depends R (>= 4.1.0)
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, BiocStyle, devtools, knitr, magick, pheatmap, rmarkdown, testthat (>= 3.1.6)
Linking To
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Depends On Me
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Package Archives

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

Source Package CaDrA_1.1.1.tar.gz
Windows Binary CaDrA_1.1.1.zip (64-bit only)
macOS Binary (x86_64) CaDrA_1.1.1.tgz
macOS Binary (arm64) CaDrA_1.1.1.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