Package: systemPipeTools 1.21.0

Daniela Cassol

systemPipeTools: Tools for data visualization

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.

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

systemPipeTools_1.21.0.tar.gz
systemPipeTools_1.21.0.zip(r-4.7)systemPipeTools_1.21.0.zip(r-4.6)systemPipeTools_1.21.0.zip(r-4.5)
systemPipeTools_1.21.0.tgz(r-4.6-any)systemPipeTools_1.21.0.tgz(r-4.5-any)
systemPipeTools_1.21.0.tar.gz(r-4.7-any)systemPipeTools_1.21.0.tar.gz(r-4.6-any)
systemPipeTools_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
systemPipeTools/json (API)
NEWS

# Install 'systemPipeTools' in R:
install.packages('systemPipeTools', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:systemPipeTools-1.21.0(bioc 3.24)systemPipeTools-1.20.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

infrastructuredataimportsequencingqualitycontrolreportwritingexperimentaldesignclusteringdifferentialexpressionmultidimensionalscalingprincipalcomponent

4.00 score 9 scripts 296 downloads 11 exports 121 dependencies

Last updated from:a2d187e3ac. Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE222
linux-devel-x86_64WARNING389
source / vignettesOK331
linux-release-x86_64WARNING362
macos-release-arm64WARNING245
macos-oldrel-arm64WARNING223
windows-develWARNING350
windows-releaseWARNING335
windows-oldrelWARNING283
wasm-releaseOK176

Exports:exploreDDSexploreDDSplotGLMplothclustplotheatMaplotMAplotMDSplotPCAplotshowDTtSNEplotvolcanoplot

Dependencies:abindapeaplotaskpassbase64encBHBiobaseBiocGenericsBiocParallelbslibcachemclicodetoolscpp11crayoncrosstalkcurldata.tableDelayedArrayDESeq2digestdplyrDTevaluatefarverfastmapfontawesomefontBitstreamVerafontLiberationfontquiverforcatsformatRfsfutile.loggerfutile.optionsgdtoolsgenericsGenomicRangesGGallyggfunggiraphggplot2ggplotifyggrepelggstatsggtreeglmpcagluegridGraphicsgtablehighrhmshtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimenlmeopensslotelpatchworkpheatmappillarpkgconfigplotlyprettyunitsprogresspromisespurrrR6rappdirsRColorBrewerRcppRcppArmadillorlangrmarkdownRtsneS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsyssystemfontstibbletidyrtidyselecttidytreetinytextreeioutf8vctrsviridisLitewithrxfunXVectoryamlyulab.utils

systemPipeTools: Data Visualizations

Author: Daniela Cassol and Thomas Girke

Rendered fromsystemPipeTools.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2021-05-10
Started: 2021-04-22