Package: TBSignatureProfiler
Title: Profile RNA-Seq Data Using TB Pathway Signatures
Version: 1.25.0
Authors@R: c(
    person("Kiloni", "Quiles", , "kiloni.quiles@rutgers.edu", role = c("cre"), 
            comment = c(ORCID = "0000-0002-7521-5255")),
    person("Aubrey R.", "Odom", , "aodom@bu.edu", role = c("aut", "dtm"),
           comment = c(ORCID = "0000-0001-7113-7598")),
    person("David", "Jenkins", , "dfj@bu.edu", role = c("aut", "org"),
           comment = c(ORCID = "0000-0002-7451-4288")),
    person("Xutao", "Wang", , "xutaow@bu.edu", role = "aut"),
    person("Yue", "Zhao", , "yuezh@bu.edu", role = "ctb",
           comment = c(ORCID = "0000-0001-5257-5103")),
    person("Christian", "Love", , "clove@bu.edu", role = "ctb"),
    person("W. Evan", "Johnson", , "wej@bu.edu", role = "aut")
  )
Description: Gene signatures of TB progression, TB disease, and other
        TB disease states have been validated and published previously.
        This package aggregates known signatures and provides
        computational tools to enlist their usage on other datasets.
        The TBSignatureProfiler makes it easy to profile RNA-Seq data
        using these signatures and includes common signature profiling
        tools including ASSIGN, GSVA, and ssGSEA. Original models for
        some gene signatures are also available.  A shiny app provides
        some functionality alongside for detailed command line
        accessibility.
License: MIT + file LICENSE
URL: https://github.com/wejlab/TBSignatureProfiler,
        https://wejlab.github.io/TBSignatureProfiler-docs/
BugReports: https://github.com/wejlab/TBSignatureProfiler/issues
Depends: R (>= 4.4.0)
Imports: ASSIGN (>= 1.23.1), BiocParallel, ComplexHeatmap, DESeq2, DT,
        edgeR, gdata, ggplot2, glmnet, GSVA (>= 1.51.3), HGNChelper,
        magrittr, methods, pROC, RColorBrewer, reshape2, ROCit,
        S4Vectors, singscore, stats, SummarizedExperiment, tibble
Suggests: BiocStyle, caret, circlize, class, covr, dplyr, e1071,
        impute, knitr, lintr, MASS, plyr, randomForest, rmarkdown,
        shiny, spelling, sva, testthat
VignetteBuilder: knitr
biocViews: GeneExpression, DifferentialExpression
Encoding: UTF-8
Language: en-US
LazyData: TRUE
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Config/pak/sysreqs: cmake make libmagick++-dev gsfonts libicu-dev
        libpng-dev libuv1-dev libxml2-dev libssl-dev perl zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:52:35 UTC
RemoteUrl: https://github.com/bioc/TBSignatureProfiler
RemoteRef: HEAD
RemoteSha: 3f57ba4f0c40662184264c03cc34753829462807
NeedsCompilation: no
Packaged: 2026-07-04 08:42:44 UTC; root
Author: Kiloni Quiles [cre] (ORCID: <https://orcid.org/0000-0002-7521-5255>),
  Aubrey R. Odom [aut, dtm] (ORCID:
    <https://orcid.org/0000-0001-7113-7598>),
  David Jenkins [aut, org] (ORCID:
    <https://orcid.org/0000-0002-7451-4288>),
  Xutao Wang [aut],
  Yue Zhao [ctb] (ORCID: <https://orcid.org/0000-0001-5257-5103>),
  Christian Love [ctb],
  W. Evan Johnson [aut]
Maintainer: Kiloni Quiles <kiloni.quiles@rutgers.edu>