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miaViz

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

Microbiome Analysis Plotting and Visualization

Bioconductor version: Development (3.18)

The miaViz package implements functions to visualize TreeSummarizedExperiment objects especially in the context of microbiome analysis. Part of the mia family of R/Bioconductor packages.

Author: Tuomas Borman [aut, cre] , Felix G.M. Ernst [aut] , Leo Lahti [aut]

Maintainer: Tuomas Borman <tuomas.v.borman at utu.fi>

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

Installation

To install this package, start R (version "4.3") and enter: 

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

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

BiocManager::install("miaViz")

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("miaViz")
miaViz HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Microbiome, Software, Visualization
Version 1.9.0
In Bioconductor since BioC 3.13 (R-4.1) (2 years)
License Artistic-2.0 | file LICENSE
Depends R (>= 4.0), SummarizedExperiment, TreeSummarizedExperiment, mia(>= 0.99), ggplot2, ggraph (>= 2.0)
Imports methods, stats, S4Vectors, BiocGenerics, BiocParallel, DelayedArray, scater, ggtree, ggnewscale, viridis, tibble, tidytree, tidygraph, rlang, purrr, tidyr, dplyr, ape, DirichletMultinomial
Linking To
Suggests knitr, rmarkdown, BiocStyle, testthat, patchwork, vegan, microbiomeDataSets
System Requirements
Enhances
URL
See More
Depends On Me
Imports Me
Suggests Me miaSim
Links To Me
Build Report  

Package Archives

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

Source Package miaViz_1.9.0.tar.gz
Windows Binary miaViz_1.9.0.zip
macOS Binary (x86_64) miaViz_1.9.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/miaViz
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/miaViz
Bioc Package Browser https://code.bioconductor.org/browse/miaViz/
Package Short Url https://bioconductor.org/packages/miaViz/
Package Downloads Report Download Stats