systemPipeTools
This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see systemPipeTools.
Tools for data visualization
Bioconductor version: 3.14
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 gmail.com>
citation("systemPipeTools")):
Installation
To install this package, start R (version "4.1") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("systemPipeTools")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("systemPipeTools")| systemPipeTools: Data Visualizations | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, DataImport, DifferentialExpression, ExperimentalDesign, Infrastructure, MultidimensionalScaling, PrincipalComponent, QualityControl, ReportWriting, Sequencing, Software |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3 years) |
| License | Artistic-2.0 |
| Depends | |
| Imports | DESeq2, GGally, Rtsne, SummarizedExperiment, ape, dplyr, ggplot2, ggrepel, ggtree, glmpca, pheatmap, plotly, tibble, magrittr, DT, stats |
| System Requirements | |
| URL |
See More
| Suggests | systemPipeR, knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), BiocGenerics, Biostrings, methods |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | systemPipeTools_1.2.0.tar.gz |
| Windows Binary | systemPipeTools_1.2.0.zip |
| macOS 10.13 (High Sierra) | systemPipeTools_1.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/systemPipeTools |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/systemPipeTools |
| Bioc Package Browser | https://code.bioconductor.org/browse/systemPipeTools/ |
| Package Short Url | https://bioconductor.org/packages/systemPipeTools/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.14 | Source Archive |