systemPipeTools
Tools for data visualization
Bioconductor version: 3.23 · Package version: 1.20.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("systemPipeTools")Details
| Maintainer | Daniela Cassol <danicassol@gmail.com> |
| Author | Daniela Cassol [aut, cre], Ponmathi Ramasamy [aut], Le Zhang [aut], Thomas Girke [aut] |
| License | Artistic-2.0 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Clustering, DataImport, DifferentialExpression, ExperimentalDesign, Infrastructure, MultidimensionalScaling, PrincipalComponent, QualityControl, ReportWriting, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/systemPipeTools/ |
Citation
From within R, enter citation("systemPipeTools"):
Daniela Cassol, Ponmathi Ramasamy, Le Zhang, Thomas Girke. systemPipeTools: Tools for data visualization. doi:10.18129/B9.bioc.systemPipeTools, R package version 1.20.0, https://bioconductor.org/packages/systemPipeTools.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | systemPipeTools_1.20.0.tar.gz |
| Windows binary (x86_64) | systemPipeTools_1.20.0.zip |
| macOS binary (arm64) | systemPipeTools_1.20.0.tgz |
| macOS binary (x86_64) | systemPipeTools_1.20.0.tgz |
Dependencies
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