iSEEtree

This is the development version of iSEEtree; to use it, please install the devel version of Bioconductor.

Interactive visualisation for microbiome data


Bioconductor version: Development (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] , Ely Seraidarian [ctb] , Leo Lahti [aut]

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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews GUI, Microbiome, ShinyApps, Software, Visualization
Version 0.99.6
In Bioconductor since BioC 3.20 (R-4.4)
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
See More
Suggests BiocStyle, knitr, RefManageR, remotes, rmarkdown, scater, testthat (>= 3.0.0), vegan
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
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Build Report Build Report

Package Archives

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

Source Package iSEEtree_0.99.6.tar.gz
Windows Binary iSEEtree_0.99.6.zip
macOS Binary (x86_64) iSEEtree_0.99.6.tgz
macOS Binary (arm64) iSEEtree_0.99.6.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/
Package Downloads Report Download Stats