iSEEtree

This package is for version 3.20 of Bioconductor; for the stable, up-to-date release version, see iSEEtree.

Interactive visualisation for microbiome data

Bioconductor version: 3.20

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.

Author: Giulio Benedetti [aut, cre] ORCID iD ORCID: 0000-0002-8732-7692 , Ely Seraidarian [ctb] ORCID iD ORCID: 0009-0008-8602-093X , Leo Lahti [aut] ORCID iD ORCID: 0000-0001-5537-637X

Maintainer: Giulio Benedetti <giulio.benedetti at utu.fi>

Citation (from within R, enter citation("iSEEtree")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("iSEEtree")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("iSEEtree")

iSEEtree HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, GUI, Microbiome, ShinyApps, Software, Visualization

Version 1.0.0

In Bioconductor since BioC 3.20 (R-4.4) (< 6 months)

License Artistic-2.0

Depends R (>= 4.4.0), iSEE

Imports grDevices, methods, miaViz, S4Vectors, shiny, mia, shinyWidgets, SingleCellExperiment, SummarizedExperiment, TreeSummarizedExperiment, utils

System Requirements

URL https://github.com/microbiome/iSEEtree

Bug Reports https://github.com/microbiome/iSEEtree/issues

Suggests biomformat, BiocStyle, knitr, MGnifyR, RefManageR, remotes, rmarkdown, scater, testthat (>= 3.0.0), vegan

Linking To

Enhances

Depends On Me

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Links To Me

Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package iSEEtree_1.0.0.tar.gz

Windows Binary (x86_64) iSEEtree_1.0.0.zip

macOS Binary (x86_64) iSEEtree_1.0.0.tgz

macOS Binary (arm64) iSEEtree_1.0.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/iSEEtree

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/iSEEtree

Bioc Package Browser https://code.bioconductor.org/browse/iSEEtree/

Package Short Url https://bioconductor.org/packages/iSEEtree/

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