Package: ASSIGN
Type: Package
Title: Adaptive Signature Selection and InteGratioN (ASSIGN)
Version: 1.46.0
Date: 2014-10-30
Author: Ying Shen, Andrea H. Bild, W. Evan Johnson, and Mumtehena
        Rahman
Authors@R: c(person(given="Ying", family="Shen", email="yshen3@bu.edu", role=c("aut")),
             person(given=c("Andrea","H."), family="Bild", email="abild@coh.org", role=c("aut")),
             person(given=c("W.", "Evan"), family="Johnson", email="wej@bu.edu", role=c("aut"),
                    comment = c(ORCID = "0000-0002-6247-6595")),
             person(given="Mumtehena", family="Rahman", email="moom.rahman@utah.edu", role=c("aut")),
             person(given="David", family="Jenkins", email="dfj@bu.edu", role=c("aut","cre"),
                    comment = c(ORCID = "0000-0002-7451-4288")))
Maintainer: Ying Shen <yshen3@bu.edu>, W. Evan Johnson <wej@bu.edu>,
 David Jenkins <dfj@bu.edu>, Mumtehena Rahman
 <moom.rahman@utah.edu>
Depends: R (>= 3.4)
Description: 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.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: gplots, graphics, grDevices, msm, Rlab, stats, sva, utils,
        ggplot2, yaml
biocViews: Software, GeneExpression, Pathways, Bayesian
Suggests: testthat, BiocStyle, lintr, knitr, rmarkdown
RoxygenNote: 7.1.0
VignetteBuilder: knitr
URL: https://compbiomed.github.io/ASSIGN/
BugReports: https://github.com/compbiomed/ASSIGN/issues
Config/pak/sysreqs: libpng-dev libxml2-dev libssl-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:18:49 UTC
RemoteUrl: https://github.com/bioc/ASSIGN
RemoteRef: RELEASE_3_22
RemoteSha: 09ba42143155ec7127a744bc8fd66461725e938c
NeedsCompilation: no
Packaged: 2026-02-24 08:16:10 UTC; root
Built: R 4.5.2; ; 2026-02-24 08:17:53 UTC; windows
