Package: iSEEtree 1.1.0

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_1.1.0.tar.gz
iSEEtree_1.1.0.zip(r-4.5)iSEEtree_1.1.0.zip(r-4.4)
iSEEtree_1.1.0.tgz(r-4.4-any)
iSEEtree_1.1.0.tar.gz(r-4.5-noble)iSEEtree_1.1.0.tar.gz(r-4.4-noble)
iSEEtree_1.1.0.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-1.1.0(bioc 3.21)iSEEtree-1.0.0(bioc 3.20)

microbiome software visualization gui shinyapps dataimport shiny-apps visualisation

5.76 score 3 stars 5 scripts 166 downloads 7 exports 220 dependencies

Last updated 2 months agofrom:250f5fdd8b. Checks:OK: 2 NOTE: 1 WARNING: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win	WARNING	Oct 31 2024
R-4.5-linux	NOTE	Oct 31 2024
R-4.4-win	WARNING	Oct 31 2024
R-4.4-mac	OK	Oct 31 2024

Exports:AbundanceDensityPlot AbundancePlot ColumnTreePlot iSEE LoadingPlot RDAPlot RowTreePlot

Dependencies:abind ape aplot askpass assorthead backports base64enc beachmat beeswarm BH Biobase BiocBaseUtils BiocGenerics BiocNeighbors BiocParallel BiocSingular Biostrings bluster boot bslib cachem Cairo checkmate circlize cli clue cluster codetools colorspace colourpicker commonmark ComplexHeatmap cpp11 crayon crosstalk curl data.table DBI DECIPHER decontam DelayedArray DelayedMatrixStats digest DirichletMultinomial doParallel dplyr dqrng DT evaluate fansi farver fastmap FNN fontawesome foreach foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges GetoptLong ggbeeswarm ggforce ggfun ggnewscale ggplot2 ggplotify ggraph ggrastr ggrepel ggtree GlobalOptions glue graphlayouts gridExtra gridGraphics gtable highr Hmisc htmlTable htmltools htmlwidgets httpuv httr igraph IRanges irlba iSEE isoband iterators janeaustenr jquerylib jsonlite knitr labeling lambda.r later lattice lazyeval lifecycle listviewer lme4 lpSolve magrittr MASS Matrix MatrixGenerics matrixStats mediation memoise mgcv mia miaViz mime miniUI minqa MultiAssayExperiment munsell mvtnorm nlme nloptr nnet openssl openxlsx patchwork permute pheatmap pillar pkgconfig plyr png polyclip promises purrr R.methodsS3 R.oo R.utils R6 ragg rappdirs rbiom RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppML RcppParallel RcppProgress reshape2 rintrojs rjson rlang rmarkdown rpart RSpectra rstudioapi rsvd Rtsne S4Arrays S4Vectors sandwich 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 UCSC.utils utf8 uwot vctrs vegan vipor viridis viridisLite withr xfun xtable XVector yaml yulab.utils zip zlibbioc zoo

iSEEtree: interactive exploration of microbiome data

Giulio Benedetti

Rendered fromiSEEtree.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-10-28
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