iSEEtree

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20

Interactive visualisation for microbiome data

Bioconductor version: Development (3.24)

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

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

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

Giulio Benedetti, Leo Lahti. iSEEtree: Interactive visualisation for microbiome data. doi:10.18129/B9.bioc.iSEEtree, R package version 1.7.0, https://bioconductor.org/packages/iSEEtree.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, GUI, Microbiome, ShinyApps, Software, Visualization
Version	1.7.0
In Bioconductor since	BioC 3.20 (R-4.4) (2 years)
License	Artistic-2.0
Depends	R (>= 4.4.0), iSEE (>= 2.19.4)
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

Suggests	biomformat, BiocStyle, knitr, RefManageR, remotes, rmarkdown, scater, testthat (>= 3.0.0), vegan
Linking To
Enhances
Depends On Me
Imports Me	miaDash
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	iSEEtree_1.7.0.tar.gz
Windows Binary (x86_64)	iSEEtree_1.7.0.zip
macOS Binary (big-sur-x86_64)	iSEEtree_1.7.0.tgz
macOS Binary (sonoma-arm64)	iSEEtree_1.7.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/iSEEtree
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/iSEEtree
Package Short Url	https://bioconductor.org/packages/iSEEtree/
Package Downloads Report	Download Stats