miaViz

Microbiome Analysis Plotting and Visualization


Bioconductor version: Release (3.19)

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] , Basil Courbayre [ctb], Giulio Benedetti [ctb]

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

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

Installation

To install this package, start R (version "4.4") and enter:


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

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 1.12.0
In Bioconductor since BioC 3.13 (R-4.1) (3.5 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, ggrepel, SingleCellExperiment
System Requirements
URL
See More
Suggests knitr, rmarkdown, BiocStyle, testthat, patchwork, vegan, microbiomeDataSets, bluster
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me MGnifyR, miaSim
Links To Me
Build Report Build Report

Package Archives

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

Source Package miaViz_1.12.0.tar.gz
Windows Binary miaViz_1.12.0.zip (64-bit only)
macOS Binary (x86_64) miaViz_1.12.0.tgz
macOS Binary (arm64) miaViz_1.12.0.tgz
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