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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 (3.22)

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 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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, GUI, Microbiome, ShinyApps, Software, Visualization
Version 1.3.2
In Bioconductor since BioC 3.20 (R-4.4) (1 year)
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
See More
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

Package Archives

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

Source Package iSEEtree_1.3.2.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