CaDrA
This is the development version of CaDrA; for the stable release version, see CaDrA.
Candidate Driver Analysis
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Reina Chau <rchau88 at bu.edu>
citation("CaDrA")):
Installation
To install this package, start R (version "4.5") 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")| 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 | 1.5.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (1 year) |
| License | GPL-3 + file LICENSE |
| Depends | R (>= 4.4.0) |
| Imports | doParallel, ggplot2, gplots, graphics, grid, gtable, knnmi, 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_1.5.0.tar.gz |
| Windows Binary (x86_64) | CaDrA_1.5.0.zip (64-bit only) |
| macOS Binary (x86_64) | CaDrA_1.5.0.tgz |
| macOS Binary (arm64) | CaDrA_1.5.0.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 |