CaDrA
This is thereleased version of CaDrA; for the devel version, seeCaDrA.
Candidate Driver Analysis
Bioconductor version: Release (3.22)
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: 0000-0003-3012-1404, Katia Bulekova [aut] ORCID: 0000-0003-1560-2146, Vinay Kartha [aut], Stefano Monti [aut] ORCID: 0000-0002-9376-0660
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")BiocManager::install("CaDrA")For older versions of R, please refer to the appropriateBioconductor 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 | 1.8.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (2 years) |
| License | GPL-3 + fileLICENSE |
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | CaDrA_1.8.0.tar.gz |
| Windows Binary (x86_64) | CaDrA_1.8.0.zip |
| macOS Binary (x86_64) | CaDrA_1.8.0.tgz |
| macOS Binary (arm64) | CaDrA_1.8.0.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 |