Package: systemPipeTools
Title: Tools for data visualization
Version: 1.18.0
Date: 2021-05-11
Authors@R: c(
    person(given = "Daniela", family = "Cassol", role = c("aut", "cre"), email = "danicassol@gmail.com"),
    person(given = "Ponmathi", family = "Ramasamy", role = c("aut"), email = "prama008@ucr.edu"),
    person(given = "Le", family = "Zhang", role = c("aut"), email = "le.zhang001@email.ucr.edu"),
    person(given = "Thomas", family = "Girke", role = c("aut"), email = "thomas.girke@ucr.edu"))
Description: systemPipeTools package extends the widely used systemPipeR (SPR) workflow environment with an enhanced toolkit for data visualization, including utilities to automate the data visualizaton for analysis of differentially expressed genes (DEGs). systemPipeTools provides data transformation and data exploration functions via scatterplots, hierarchical clustering heatMaps, principal component analysis, multidimensional scaling, generalized principal components, t-Distributed Stochastic Neighbor embedding (t-SNE), and MA and volcano plots. All these utilities can be integrated with the modular design of the systemPipeR environment that allows users to easily substitute any of these features and/or custom with alternatives.
Imports: DESeq2, GGally, Rtsne, SummarizedExperiment, ape, dplyr,
        ggplot2, ggrepel, ggtree, glmpca, pheatmap, plotly, tibble,
        magrittr, DT, stats
Suggests: systemPipeR, knitr, BiocStyle, rmarkdown, testthat (>=
        3.0.0), BiocGenerics, Biostrings, methods
biocViews: Infrastructure, DataImport, Sequencing, QualityControl,
        ReportWriting, ExperimentalDesign, Clustering,
        DifferentialExpression, MultidimensionalScaling,
        PrincipalComponent
License: Artistic-2.0
Encoding: UTF-8
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
Config/testthat/edition: 3
git_url: https://git.bioconductor.org/packages/systemPipeTools
git_branch: RELEASE_3_22
git_last_commit: c54c5be
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.22
Date/Publication: 2025-10-30
NeedsCompilation: no
Packaged: 2025-10-30 21:57:30 UTC; biocbuild
Author: Daniela Cassol [aut, cre],
  Ponmathi Ramasamy [aut],
  Le Zhang [aut],
  Thomas Girke [aut]
Maintainer: Daniela Cassol <danicassol@gmail.com>
Built: R 4.5.1; ; 2025-10-31 03:19:44 UTC; unix
