ASSIGN
This is the development version of ASSIGN; for the stable release version, see ASSIGN.
Adaptive Signature Selection and InteGratioN (ASSIGN)
Bioconductor version: Development (3.24)
ASSIGN is a computational tool to evaluate the pathway deregulation/activation status in individual patient samples. ASSIGN employs a flexible Bayesian factor analysis approach that adapts predetermined pathway signatures derived either from knowledge-based literature or from perturbation experiments to the cell-/tissue-specific pathway signatures. The deregulation/activation level of each context-specific pathway is quantified to a score, which represents the extent to which a patient sample encompasses the pathway deregulation/activation signature.
Author: Ying Shen, Andrea H. Bild, W. Evan Johnson, and Mumtehena Rahman
Maintainer: Ying Shen <yshen3 at bu.edu>, W. Evan Johnson <wej at bu.edu>, David Jenkins <dfj at bu.edu>, Mumtehena Rahman <moom.rahman at utah.edu>
citation("ASSIGN")):
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("ASSIGN")
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("ASSIGN")| Primer | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Bayesian, GeneExpression, Pathways, Software |
| Version | 1.49.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (12.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.4) |
| Imports | gplots, graphics, grDevices, msm, Rlab, stats, sva, utils, ggplot2, yaml |
| System Requirements | |
| URL | https://compbiomed.github.io/ASSIGN/ |
| Bug Reports | https://github.com/compbiomed/ASSIGN/issues |
See More
| Suggests | testthat, BiocStyle, lintr, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | TBSignatureProfiler |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ASSIGN_1.49.0.tar.gz |
| Windows Binary (x86_64) | ASSIGN_1.49.0.zip |
| macOS Binary (big-sur-x86_64) | ASSIGN_1.49.0.tgz |
| macOS Binary (sonoma-arm64) | ASSIGN_1.49.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ASSIGN |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ASSIGN |
| Bioc Package Browser | https://code.bioconductor.org/browse/ASSIGN/ |
| Package Short Url | https://bioconductor.org/packages/ASSIGN/ |
| Package Downloads Report | Download Stats |