DOI: 10.18129/B9.bioc.ASSIGN  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see ASSIGN.

Adaptive Signature Selection and InteGratioN (ASSIGN)

Bioconductor version: 3.17

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>, W. Evan Johnson <wej at>, David Jenkins <dfj at>, Mumtehena Rahman <moom.rahman at>

Citation (from within R, enter citation("ASSIGN")):


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biocViews Bayesian, GeneExpression, Pathways, Software
Version 1.36.0
In Bioconductor since BioC 2.14 (R-3.1) (9.5 years)
License MIT + file LICENSE
Depends R (>= 3.4)
Imports gplots, graphics, grDevices, msm, Rlab, stats, sva, utils, ggplot2, yaml
Suggests testthat, BiocStyle, lintr, knitr, rmarkdown
Depends On Me
Imports Me TBSignatureProfiler
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Links To Me
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