Package: TBSignatureProfiler
Title: Profile RNA-Seq Data Using TB Pathway Signatures
Version: 1.8.0
Authors@R: c(
    person("Aubrey", "Odom-Mabey", , "aodom@bu.edu", role = c("aut", "cre", "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/compbiomed/TBSignatureProfiler
        https://compbiomed.github.io/TBSignatureProfiler-docs/
BugReports: https://github.com/compbiomed/TBSignatureProfiler/issues
Depends: R (>= 4.1)
Imports: ASSIGN (>= 1.23.1), BiocGenerics, BiocParallel,
        ComplexHeatmap, DESeq2, DT, edgeR, gdata, ggplot2, GSVA,
        magrittr, methods, RColorBrewer, reshape2, rlang, ROCit,
        S4Vectors, singscore, stats, SummarizedExperiment
Suggests: BiocStyle, caret, circlize, class, covr, dplyr, e1071,
        glmnet, HGNChelper, impute, knitr, lintr, MASS, plyr, pROC,
        randomForest, rmarkdown, shiny, spelling, sva, testthat
VignetteBuilder: knitr
biocViews: GeneExpression, DifferentialExpression
Encoding: UTF-8
Language: en-US
LazyData: TRUE
RoxygenNote: 7.1.2
git_url: https://git.bioconductor.org/packages/TBSignatureProfiler
git_branch: RELEASE_3_15
git_last_commit: 0ea7c4c
git_last_commit_date: 2022-04-26
Date/Publication: 2022-04-26
NeedsCompilation: no
Packaged: 2022-04-27 01:31:57 UTC; biocbuild
Author: Aubrey Odom-Mabey [aut, cre, dtm]
    (<https://orcid.org/0000-0001-7113-7598>),
  David Jenkins [aut, org] (<https://orcid.org/0000-0002-7451-4288>),
  Xutao Wang [aut],
  Yue Zhao [ctb] (<https://orcid.org/0000-0001-5257-5103>),
  Christian Love [ctb],
  W. Evan Johnson [aut]
Maintainer: Aubrey Odom-Mabey <aodom@bu.edu>
Built: R 4.2.0; ; 2022-04-27 10:11:45 UTC; windows
