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systemPipeTools

This is the development version of systemPipeTools; for the stable release version, see systemPipeTools.

Tools for data visualization


Bioconductor version: Development (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 gmail.com>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF
NEWS Text

Details

biocViews Clustering, DataImport, DifferentialExpression, ExperimentalDesign, Infrastructure, MultidimensionalScaling, PrincipalComponent, QualityControl, ReportWriting, Sequencing, Software
Version 1.11.0
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_1.11.0.tar.gz
Windows Binary systemPipeTools_1.11.0.zip
macOS Binary (x86_64) systemPipeTools_1.11.0.tgz
macOS Binary (arm64) systemPipeTools_1.11.0.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