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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 data container. It provides interactive panel designs to explore hierarchical datasets, such as the microbiome and cell lines.

Author: Giulio Benedetti [aut, cre] (ORCID: ), Ely Seraidarian [ctb] (ORCID: ), Leo Lahti [aut] (ORCID: )

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

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
iSEEtree HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataImport, GUI, Microbiome, ShinyApps, Software, Visualization
Version 1.1.4
In Bioconductor since BioC 3.20 (R-4.4) (< 6 months)
License Artistic-2.0
Depends R (>= 4.4.0), iSEE(>= 2.19.2)
Imports ape, ggplot2, ggtree, grDevices, methods, miaViz, purrr, S4Vectors, shiny, mia, shinyWidgets, SingleCellExperiment, SummarizedExperiment, tidygraph, TreeSummarizedExperiment, utils
System Requirements
URL https://github.com/microbiome/iSEEtree
Bug Reports https://github.com/microbiome/iSEEtree/issues
See More
Suggests biomformat, BiocStyle, knitr, RefManageR, remotes, rmarkdown, scater, testthat (>= 3.0.0), vegan
Linking To
Enhances
Depends On Me
Imports 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_1.1.4.tar.gz
Windows Binary (x86_64) iSEEtree_1.1.4.zip
macOS Binary (x86_64) iSEEtree_1.1.4.tgz
macOS Binary (arm64) iSEEtree_1.1.4.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