iSEEtree

This is the development version of iSEEtree; for the stable release version, see iSEEtree.

Interactive visualisation for microbiome data

Bioconductor version: Development (3.21)

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: ), Ely Seraidarian [ctb] (ORCID: ), Leo Lahti [aut] (ORCID: )

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

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

Installation

To install this package, start R (version "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, GUI, Microbiome, ShinyApps, Software, Visualization
Version	1.1.0
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
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	iSEEtree_1.1.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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