Package: systemPipeTools 1.21.1

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_1.21.1.tar.gz
systemPipeTools_1.21.1.zip(r-4.7-any)systemPipeTools_1.21.1.zip(r-4.6-any)systemPipeTools_1.21.1.zip(r-4.5-any)
systemPipeTools_1.21.1.tgz(r-4.6-any)systemPipeTools_1.21.1.tgz(r-4.5-any)
systemPipeTools_1.21.1.tar.gz(r-4.7-any)systemPipeTools_1.21.1.tar.gz(r-4.6-any)
systemPipeTools_1.21.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
systemPipeTools/json (API)

# 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.

infrastructure dataimport sequencing qualitycontrol reportwriting experimentaldesign clustering differentialexpression multidimensionalscaling principalcomponent

4.18 score 10 scripts 418 downloads 11 exports 121 dependencies

Last updated from:6cfdf7fde8. Checks:8 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	205
linux-devel	WARNING	417
source / vignettes	OK	272
linux-release	WARNING	445
macos-release	WARNING	223
macos-oldrel	WARNING	253
windows-devel	WARNING	222
windows-release	WARNING	313
windows-oldrel	WARNING	315
wasm-release	OK	178

Exports:exploreDDS exploreDDSplot GLMplot hclustplot heatMaplot MAplot MDSplot PCAplot showDT tSNEplot volcanoplot

Dependencies:abind ape aplot askpass base64enc BH Biobase BiocGenerics BiocParallel bslib cachem cli codetools cpp11 crayon crosstalk curl data.table DelayedArray DESeq2 digest dplyr DT evaluate farver fastmap fontawesome fontBitstreamVera fontLiberation fontquiver forcats formatR fs futile.logger futile.options gdtools generics GenomicRanges GGally ggfun ggiraph ggplot2 ggplotify ggrepel ggstats ggtree glmpca glue gridGraphics gtable highr hms htmltools htmlwidgets httr IRanges isoband jquerylib jsonlite knitr labeling lambda.r later lattice lazyeval lifecycle locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mime nlme openssl otel patchwork pheatmap pillar pkgconfig plotly prettyunits progress promises purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo rlang rmarkdown Rtsne S4Arrays S4Vectors S7 sass scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys systemfonts tibble tidyr tidyselect tidytree tinytex treeio utf8 vctrs viridisLite withr xfun XVector yaml yulab.utils

systemPipeTools: Data Visualizations

Rendered fromsystemPipeTools.Rmdusingknitr::rmarkdown

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

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

Package: systemPipeTools 1.21.1

systemPipeTools: Tools for data visualization

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