Package: systemPipeTools
Title: Tools for data visualization
Version: 1.21.0
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
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev make libicu-dev libpng-dev libuv1-dev
        libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:56:18 UTC
RemoteUrl: https://github.com/bioc/systemPipeTools
RemoteRef: HEAD
RemoteSha: a2d187e3ac2ad9e8d99215d7657f68cc59ee269b
NeedsCompilation: no
Packaged: 2026-07-04 22:09:41 UTC; root
Author: Daniela Cassol [aut, cre],
  Ponmathi Ramasamy [aut],
  Le Zhang [aut],
  Thomas Girke [aut]
Maintainer: Daniela Cassol <danicassol@gmail.com>