Package: SingscoreAMLMutations
Title: Using singscore to predict mutations in AML from transcriptomic
        signatures
Version: 1.28.0
Authors@R: 
    c(
      person(
        "Dharmesh",
        "Bhuva",
        "D.",
        email = "bhuva.d@wehi.edu.au",
        role = c("aut", "cre"),
        comment = c(ORCID = '0000-0002-6398-9157')
      ),
      person(
        "Momeneh",
        "Foroutan",
        email = "foroutan.m@wehi.edu.au",
        role = c("aut"),
        comment = c(ORCID = '0000-0002-1440-0457')
      ),
      person(
        "Yi",
        "Xie",
        email = "xie.y@wehi.edu.au",
        role = c("aut"),
        comment = c(ORCID = '0000-0002-1938-4089')
      ),
      person(
        "Ruqian",
        "Lyu",
        email = "lyu.r@wehi.edu.au",
        role = c("aut"),
        comment = c(ORCID = '')
      ),
      person(
        "Malvika",
        "Kharbanda",
        email = "kharbanda.m@wehi.edu.au",
        role = c("aut"),
        comment = c(ORCID = '0000-0001-9726-3023')
      ),
      person(
        "Joseph",
        "Cursons",
        email = "cursons.j@wehi.edu.au",
        role = c("aut"),
        comment = c(ORCID = '0000-0002-5053-4540')
      ),
      person(
        "Melissa",
        "Davis",
        "J.",
        email = "davis.m@wehi.edu.au",
        role = c("aut"),
        comment = c(ORCID = '0000-0003-4864-7033')
      )
    )
Description: This workflow package shows how transcriptomic signatures
        can be used to infer phenotypes. The workflow begins by showing
        how the TCGA AML transcriptomic data can be downloaded and
        processed using the TCGAbiolinks packages. It then shows how
        samples can be scored using the singscore package and
        signatures from the MSigDB. Finally, the predictive capacity of
        scores in the context of predicting a specific mutation in AML
        is shown.The workflow exhibits the interplay of Bioconductor
        packages to achieve a gene-set level analysis.
License: Artistic-2.0
Encoding: UTF-8
LazyData: true
Workflow: True
biocViews: GeneExpressionWorkflow, GenomicVariantsWorkflow,
        ImmunoOncologyWorkflow, Workflow
VignetteBuilder: knitr
Depends: R (>= 4.1.0)
Imports: dcanr, edgeR, ggplot2, gridExtra, GSEABase, mclust,
        org.Hs.eg.db, plyr, reshape2, rtracklayer, singscore,
        SummarizedExperiment, TCGAbiolinks, BiocFileCache
Suggests: knitr, rmarkdown, BiocStyle, BiocWorkflowTools, spelling
RoxygenNote: 7.2.0
Language: en-US
URL: https://github.com/DavisLaboratory/SingscoreAMLMutations
BugReports: https://github.com/DavisLaboratory/SingscoreAMLMutations/issues
Config/pak/sysreqs: cmake libglpk-dev make libbz2-dev libicu-dev
        liblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev
        libx11-dev xz-utils zlib1g-dev
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28 12:43:31 UTC
RemoteUrl: https://github.com/bioc/SingscoreAMLMutations
RemoteRef: RELEASE_3_23
RemoteSha: 40a99957f97ff365ad8f7f9de1d463ad2ee5ae3f
NeedsCompilation: no
Packaged: 2026-10-04 17:16:31 UTC; root
Author: Dharmesh D. Bhuva [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-6398-9157>),
  Momeneh Foroutan [aut] (ORCID: <https://orcid.org/0000-0002-1440-0457>),
  Yi Xie [aut] (ORCID: <https://orcid.org/0000-0002-1938-4089>),
  Ruqian Lyu [aut],
  Malvika Kharbanda [aut] (ORCID:
    <https://orcid.org/0000-0001-9726-3023>),
  Joseph Cursons [aut] (ORCID: <https://orcid.org/0000-0002-5053-4540>),
  Melissa J. Davis [aut] (ORCID: <https://orcid.org/0000-0003-4864-7033>)
Maintainer: Dharmesh D. Bhuva <bhuva.d@wehi.edu.au>