Package: iSEEtree 1.1.2

Giulio Benedetti

iSEEtree: Interactive visualisation for microbiome data

iSEEtree is an extension of iSEE for the TreeSummarizedExperiment. It leverages the functionality from the miaViz package for microbiome data visualisation to create panels that are specific for TreeSummarizedExperiment objects. Not surprisingly, it also depends on the generic panels from iSEE.

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

iSEEtree_1.1.2.tar.gz
iSEEtree_1.1.2.zip(r-4.5)iSEEtree_1.1.2.zip(r-4.4)
iSEEtree_1.1.2.tgz(r-4.4-any)
iSEEtree_1.1.2.tar.gz(r-4.5-noble)iSEEtree_1.1.2.tar.gz(r-4.4-noble)
iSEEtree_1.1.2.tgz(r-4.4-emscripten)
iSEEtree.pdf |iSEEtree.html✨
iSEEtree/json (API)
NEWS

# Install 'iSEEtree' in R:

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

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

On BioConductor:iSEEtree-1.1.2(bioc 3.21)iSEEtree-1.0.0(bioc 3.20)

microbiome software visualization gui shinyapps dataimport shiny-apps visualisation

5.93 score 3 stars 5 scripts 156 downloads 7 exports 217 dependencies

Last updated 2 months agofrom:628462cdb2. Checks:3 OK, 2 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 29 2025
R-4.5-win	NOTE	Jan 29 2025
R-4.5-linux	NOTE	Jan 29 2025
R-4.4-win	OK	Jan 29 2025
R-4.4-mac	OK	Jan 29 2025

Exports:AbundanceDensityPlot AbundancePlot ColumnTreePlot iSEE LoadingPlot RDAPlot RowTreePlot

Dependencies:abind ape aplot askpass assorthead base64enc beachmat beeswarm BH Biobase BiocBaseUtils BiocGenerics BiocNeighbors BiocParallel BiocSingular Biostrings bit bit64 bluster bslib cachem Cairo cellranger circlize cli clipr clue cluster codetools colorspace colourpicker commonmark ComplexHeatmap cpp11 crayon crosstalk curl DBI DECIPHER decontam DelayedArray DelayedMatrixStats digest DirichletMultinomial doParallel dplyr dqrng DT emmeans estimability evaluate fansi farver fastmap fillpattern FNN fontawesome foreach formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges GetoptLong ggbeeswarm ggforce ggfun ggnewscale ggplot2 ggplotify ggraph ggrastr ggrepel ggtext ggtree GlobalOptions glue graphlayouts gridExtra gridGraphics gridtext gtable highr hms htmltools htmlwidgets httpuv httr igraph IRanges irlba iSEE isoband iterators janeaustenr jpeg jquerylib jsonlite knitr labeling lambda.r later lattice lazyeval lifecycle listviewer magrittr markdown MASS Matrix MatrixGenerics matrixStats memoise mgcv mia miaViz mime miniUI MultiAssayExperiment munsell mvtnorm nlme numDeriv openssl parallelly patchwork permute pheatmap pillar pkgconfig plyr png polyclip prettyunits progress promises purrr R6 ragg rappdirs rbiom RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppML RcppProgress readr readxl rematch reshape2 rintrojs rjson rlang rmarkdown RSpectra rsvd Rtsne S4Arrays S4Vectors sass ScaledMatrix scales scater scuttle shape shiny shinyAce shinydashboard shinyjs shinyWidgets SingleCellExperiment sitmo slam snow SnowballC sourcetools SparseArray sparseMatrixStats stringi stringr SummarizedExperiment sys systemfonts textshaping tibble tidygraph tidyr tidyselect tidytext tidytree tinytex tokenizers treeio TreeSummarizedExperiment tweenr tzdb UCSC.utils utf8 uwot vctrs vegan vipor viridis viridisLite vroom withr xfun xml2 xtable XVector yaml yulab.utils

iSEEtree: interactive exploration of microbiome data

Giulio Benedetti

Rendered fromiSEEtree.Rmdusingknitr::rmarkdownon Jan 29 2025.

Last update: 2024-12-14
Started: 2024-04-20

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Abundance density plot	AbundanceDensityPlot AbundanceDensityPlot-class
Abundance plot	AbundancePlot AbundancePlot-class
Column tree plot	ColumnTreePlot ColumnTreePlot-class
iSEE layout for TreeSE	iSEE iSEE,TreeSummarizedExperiment-method
Loading plot	LoadingPlot LoadingPlot-class
RDA plot	RDAPlot RDAPlot-class
Row tree plot	RowTreePlot RowTreePlot-class