ASSIGN
Adaptive Signature Selection and InteGratioN (ASSIGN)
Bioconductor version: 3.23 · Package version: 1.48.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ASSIGN")Details
| Maintainer | Ying Shen <yshen3@bu.edu>, W. Evan Johnson <wej@bu.edu>, David Jenkins <dfj@bu.edu>, Mumtehena Rahman <moom.rahman@utah.edu> |
| Author | Ying Shen, Andrea H. Bild, W. Evan Johnson, and Mumtehena Rahman |
| License | MIT + file LICENSE |
| URL | https://compbiomed.github.io/ASSIGN/ |
| Bug Reports | https://github.com/compbiomed/ASSIGN/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Bayesian, GeneExpression, Pathways, Software |
| Package Short Url | https://bioconductor.org/packages/ASSIGN/ |
Citation
From within R, enter citation("ASSIGN"):
Ying Shen, Andrea H. Bild, W. Evan Johnson, and Mumtehena Rahman. ASSIGN: Adaptive Signature Selection and InteGratioN (ASSIGN). doi:10.18129/B9.bioc.ASSIGN, R package version 1.48.0, https://bioconductor.org/packages/ASSIGN.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | ASSIGN_1.48.0.tar.gz |
| Windows binary (x86_64) | ASSIGN_1.48.0.zip |
| macOS binary (arm64) | ASSIGN_1.48.0.tgz |
| macOS binary (x86_64) | ASSIGN_1.48.0.tgz |
Dependencies
Depends: R (>= 3.4)
Imports: gplots, graphics, grDevices, msm, Rlab, stats, sva, utils, ggplot2, yaml
Reverse dependencies
Imports Me (1): TBSignatureProfiler