CaDrA
This is the released version of CaDrA; for the devel version, see CaDrA.
Candidate Driver Analysis
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.10.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (3 years) |
| 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_1.10.0.tar.gz |
| Windows Binary (x86_64) | CaDrA_1.10.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | CaDrA_1.10.0.tgz |
| macOS Binary (sonoma-arm64) | CaDrA_1.10.0.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 |