ASSIGN
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see ASSIGN.
Adaptive Signature Selection and InteGratioN (ASSIGN)
Bioconductor version: 3.19
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 "4.4") 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")
Details
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Follow Installation instructions to use this package in your R session.