DeMAND
This is the development version of DeMAND; for the stable release version, see DeMAND.
DeMAND
Bioconductor version: Development (3.24)
DEMAND predicts Drug MoA by interrogating a cell context specific regulatory network with a small number (N >= 6) of compound-induced gene expression signatures, to elucidate specific proteins whose interactions in the network is dysregulated by the compound.
Author: Jung Hoon Woo <jw2853 at columbia.edu>, Yishai Shimoni <ys2559 at columbia.edu>
Maintainer: Jung Hoon Woo <jw2853 at columbia.edu>, Mariano Alvarez <reef103 at gmail.com>
citation("DeMAND")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("DeMAND")
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("DeMAND")| Using DeMAND | R Script | |
| Reference Manual | ||
| LICENSE | Text |
Details
| biocViews | GeneExpression, Network, NetworkEnrichment, Software, StatisticalMethod, SystemsBiology |
| Version | 1.43.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (11 years) |
| License | file LICENSE |
| Depends | R (>= 2.14.0), KernSmooth, methods |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | |
| 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 | DeMAND_1.43.0.tar.gz |
| Windows Binary (x86_64) | DeMAND_1.43.0.zip |
| macOS Binary (big-sur-x86_64) | DeMAND_1.43.0.tgz |
| macOS Binary (sonoma-arm64) | DeMAND_1.43.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DeMAND |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DeMAND |
| Bioc Package Browser | https://code.bioconductor.org/browse/DeMAND/ |
| Package Short Url | https://bioconductor.org/packages/DeMAND/ |
| Package Downloads Report | Download Stats |