Package: systemPipeTools 1.15.0
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:
systemPipeTools_1.15.0.tar.gz
systemPipeTools_1.15.0.zip(r-4.5)systemPipeTools_1.15.0.zip(r-4.4)systemPipeTools_1.15.0.zip(r-4.3)
systemPipeTools_1.15.0.tgz(r-4.5-any)systemPipeTools_1.15.0.tgz(r-4.4-any)systemPipeTools_1.15.0.tgz(r-4.3-any)
systemPipeTools_1.15.0.tar.gz(r-4.5-noble)systemPipeTools_1.15.0.tar.gz(r-4.4-noble)
systemPipeTools_1.15.0.tgz(r-4.4-emscripten)systemPipeTools_1.15.0.tgz(r-4.3-emscripten)
systemPipeTools.pdf |systemPipeTools.html✨
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-1.15.0(bioc 3.21)systemPipeTools-1.14.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
infrastructuredataimportsequencingqualitycontrolreportwritingexperimentaldesignclusteringdifferentialexpressionmultidimensionalscalingprincipalcomponent
Last updated 5 months agofrom:05bda0ebfd. Checks:1 OK, 8 WARNING. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 28 2025 |
| R-4.5-win | WARNING | Mar 28 2025 |
| R-4.5-mac | WARNING | Mar 28 2025 |
| R-4.5-linux | WARNING | Mar 28 2025 |
| R-4.4-win | WARNING | Mar 30 2025 |
| R-4.4-mac | WARNING | Mar 28 2025 |
| R-4.4-linux | WARNING | Mar 28 2025 |
| R-4.3-win | WARNING | Mar 30 2025 |
| R-4.3-mac | WARNING | Mar 28 2025 |
Exports:exploreDDSexploreDDSplotGLMplothclustplotheatMaplotMAplotMDSplotPCAplotshowDTtSNEplotvolcanoplot
Dependencies:abindapeaplotaskpassbase64encBHBiobaseBiocGenericsBiocParallelbslibcachemclicodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDelayedArrayDESeq2digestdplyrDTevaluatefansifarverfastmapfontawesomeforcatsformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGGallyggfunggplot2ggplotifyggrepelggstatsggtreeglmpcagluegridGraphicsgtablehighrhmshtmltoolshtmlwidgetshttpuvhttrIRangesisobandjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpatchworkpheatmappillarpkgconfigplotlyplyrprettyunitsprogresspromisespurrrR6rappdirsRColorBrewerRcppRcppArmadillorlangrmarkdownRtsneS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttidytreetinytextreeioUCSC.utilsutf8vctrsviridisLitewithrxfunXVectoryamlyulab.utils
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| exploreDDS | exploreDDS |
| exploreDDSplot | exploreDDSplot |
| Dimension Reduction with GLMplot | GLMplot |
| Hierarchical Clustering Dendrogram (hclustplot) | hclustplot |
| Hierarchical Clustering HeatMap (heatMaplot) | heatMaplot |
| MAplot | MAplot |
| Multidimensional scaling with MDSplot | MDSplot |
| PCAplot | PCAplot |
| Create an HTML table using DT package with fixed columns | showDT |
| t-Distributed Stochastic Neighbor embedding with tSNEplot | tSNEplot |
| Volcano plot with 'volcanoplot' | volcanoplot |
