DART
This is the released version of DART; for the devel version, see DART.
Denoising Algorithm based on Relevance network Topology
Bioconductor version: Release (3.23)
Denoising Algorithm based on Relevance network Topology (DART) is an algorithm designed to evaluate the consistency of prior information molecular signatures (e.g in-vitro perturbation expression signatures) in independent molecular data (e.g gene expression data sets). If consistent, a pruning network strategy is then used to infer the activation status of the molecular signature in individual samples.
Author: Yan Jiao, Katherine Lawler, Andrew E Teschendorff, Charles Shijie Zheng
Maintainer: Charles Shijie Zheng <charles_zheng at live.com>
citation("DART")):
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("DART")
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("DART")| DART Tutorial | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, GraphAndNetwork, Pathways, Software |
| Version | 1.60.0 |
| In Bioconductor since | BioC 2.10 (R-2.15) (14.5 years) |
| License | GPL-2 |
| Depends | R (>= 2.10.0), igraph (>= 0.6.0) |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | breastCancerVDX, breastCancerMAINZ, Biobase |
| 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 | DART_1.60.0.tar.gz |
| Windows Binary (x86_64) | DART_1.60.0.zip |
| macOS Binary (big-sur-x86_64) | DART_1.60.0.tgz |
| macOS Binary (sonoma-arm64) | DART_1.60.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DART |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DART |
| Bioc Package Browser | https://code.bioconductor.org/browse/DART/ |
| Package Short Url | https://bioconductor.org/packages/DART/ |
| Package Downloads Report | Download Stats |