Package: TBSignatureProfiler
Title: Profile RNA-Seq Data Using TB Pathway Signatures
Version: 1.22.0
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: make libmagick++-dev gsfonts libicu-dev libpng-dev
        libxml2-dev libssl-dev perl
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:58:59 UTC
RemoteUrl: https://github.com/bioc/TBSignatureProfiler
RemoteRef: RELEASE_3_22
RemoteSha: 376376a8b8e432ac47fcd58d5a8cd09af6b4501d
NeedsCompilation: no
Packaged: 2025-11-11 18:04:12 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>
Built: R 4.5.2; ; 2025-11-12 07:49:34 UTC; windows
