ASSIGN
This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see ASSIGN.
Adaptive Signature Selection and InteGratioN (ASSIGN)
Bioconductor version: 3.14
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")):
Installation
To install this package, start R (version "4.1") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.30.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (10 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_1.30.0.tar.gz |
| Windows Binary | ASSIGN_1.30.0.zip |
| macOS 10.13 (High Sierra) | ASSIGN_1.30.0.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 |
| Old Source Packages for BioC 3.14 | Source Archive |