Package: iSEEtree 1.6.0

Giulio Benedetti

iSEEtree: Interactive visualisation for microbiome data

iSEEtree is an extension of iSEE for the TreeSummarizedExperiment data container. It provides interactive panel designs to explore hierarchical datasets, such as the microbiome and cell lines.

Authors:Giulio Benedetti [aut, cre], Ely Seraidarian [ctb], Leo Lahti [aut]

iSEEtree_1.6.0.tar.gz
iSEEtree_1.6.0.zip(r-4.7-any)iSEEtree_1.6.0.zip(r-4.6-any)iSEEtree_1.6.0.zip(r-4.5-any)
iSEEtree_1.6.0.tgz(r-4.6-any)iSEEtree_1.6.0.tgz(r-4.5-any)
iSEEtree_1.6.0.tar.gz(r-4.7-any)iSEEtree_1.6.0.tar.gz(r-4.6-any)
iSEEtree_1.6.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
iSEEtree/json (API)

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

Bug tracker:https://github.com/microbiome/iseetree/issues

On BioConductor:iSEEtree-1.7.0(bioc 3.24)iSEEtree-1.6.0(bioc 3.23)

softwarevisualizationmicrobiomeguishinyappsdataimportshiny-appsvisualisation

5.73 score 3 stars 1 packages 7 scripts 352 downloads 13 exports 187 dependencies

Last updated from:7bf798969c (on RELEASE_3_23). Checks:8 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE235
linux-develNOTE493
source / vignettesOK376
linux-releaseNOTE492
macos-releaseNOTE351
macos-oldrelNOTE283
windows-develNOTE307
windows-releaseNOTE353
windows-oldrelNOTE330
wasm-releaseOK184

Exports:.check_all_panels.check_panelAbundanceDensityPlotAbundancePlotColumnGraphPlotColumnTreePlotiSEELoadingPlotPrevalencePlotRDAPlotRowGraphPlotRowTreePlotScreePlot

Dependencies:abindapeaplotassortheadbase64encbeachmatbeeswarmBHBiobaseBiocBaseUtilsBiocGenericsBiocNeighborsBiocParallelBiocSingularBiostringsblusterbslibcachemcirclizecliclueclustercodetoolscolorspacecolourpickercommonmarkComplexHeatmapcpp11crayoncrosstalkDBIDECIPHERdecontamDelayedArrayDelayedMatrixStatsdigestDirichletMultinomialdoParalleldplyrdqrngDTecodiveevaluatefarverfastmapFNNfontawesomefontBitstreamVerafontLiberationfontquiverforeachformatRfsfutile.loggerfutile.optionsgdtoolsgenericsGenomicRangesGetoptLongggbeeswarmggforceggfunggiraphggnewscaleggplot2ggplotifyggraphggrepelggtreeGlobalOptionsgluegraphlayoutsgridExtragridGraphicsgtablehighrhtmltoolshtmlwidgetshttpuvigraphIRangesirlbaiSEEisobanditeratorsjaneaustenrjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelistviewermagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmiamiaVizmimeminiUIMultiAssayExperimentnlmeotelpatchworkpermutepheatmappillarpkgconfigplyrpngpolyclippromisespurrrR6rappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppMLRcppProgressreshape2rintrojsrjsonrlangrmarkdownRSpectrarsvdRtsneS4ArraysS4VectorsS7sassScaledMatrixscalesscaterscuttleSeqinfoshapeshinyshinyAceshinydashboardshinyjsshinyWidgetsSingleCellExperimentsitmosnowSnowballCsourcetoolsSparseArraysparseMatrixStatsstringistringrSummarizedExperimentsystemfontstibbletidygraphtidyrtidyselecttidytexttidytreetinytextokenizerstreeioTreeSummarizedExperimenttweenrutf8uwotvctrsveganviporviridisviridisLitewithrxfunxtableXVectoryamlyulab.utils

Panel Catalogue
Introduction | Compositional Analysis | Abundance plot | Abundance density plot | Prevalence plot | Feature assay plot | Complex heatmap plot | Ordination Analysis | RDA plot | Scree plot | Loading plot | Reduced dimension plot | Structural Analysis | Row/Column tree plots | Row/Column graph plots | Other panels | Row/Column tile plots | Mediation plot | Row/Column data tables | Row/Column data plots | Reproducibility | References
Rendered frompanels.Rmdusingknitr::rmarkdown

Last update: 2025-03-19
Started: 2025-03-10

iSEEtree: interactive explorer for hierarchical data
Introduction | Motivation | Panels | Compositional Analysis | Ordination Analysis | Structural Analysis | Other Panels | Tutorial | Installation | Example | Resources | Open datasets | Other tutorials | Citation | Acknowledgements | Help | Reproducibility | References
Rendered fromiSEEtree.Rmdusingknitr::rmarkdown

Last update: 2025-03-17
Started: 2024-04-20

Readme and manuals

Help Manual

Help pageTopics
Abundance density plotAbundanceDensityPlot AbundanceDensityPlot-class
Abundance plotAbundancePlot AbundancePlot-class
Column graph plotColumnGraphPlot ColumnGraphPlot-class
Column tree plotColumnTreePlot ColumnTreePlot-class
Graph plotGraphPlot GraphPlot-class
iSEE layout for TreeSEiSEE iSEE,TreeSummarizedExperiment-method
Loading plotLoadingPlot LoadingPlot-class
Prevalence plotPrevalencePlot PrevalencePlot-class
RDA plotRDAPlot RDAPlot-class
Row graph plotRowGraphPlot RowGraphPlot-class
Row tree plotRowTreePlot RowTreePlot-class
Scree plotScreePlot ScreePlot-class
Tree plotTreePlot TreePlot-class