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Tools for data visualization

Bioconductor version: Release (3.19)

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.

Author: Daniela Cassol [aut, cre], Ponmathi Ramasamy [aut], Le Zhang [aut], Thomas Girke [aut]

Maintainer: Daniela Cassol <danicassol at>

Citation (from within R, enter citation("systemPipeTools")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

systemPipeTools: Data Visualizations HTML R Script
Reference Manual PDF


biocViews Clustering, DataImport, DifferentialExpression, ExperimentalDesign, Infrastructure, MultidimensionalScaling, PrincipalComponent, QualityControl, ReportWriting, Sequencing, Software
Version 1.12.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License Artistic-2.0
Imports DESeq2, GGally, Rtsne, SummarizedExperiment, ape, dplyr, ggplot2, ggrepel, ggtree, glmpca, pheatmap, plotly, tibble, magrittr, DT, stats
System Requirements
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Suggests systemPipeR, knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), BiocGenerics, Biostrings, methods
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package systemPipeTools_1.12.0.tar.gz
Windows Binary
macOS Binary (x86_64) systemPipeTools_1.12.0.tgz
macOS Binary (arm64) systemPipeTools_1.12.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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Old Source Packages for BioC 3.19 Source Archive