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Bioconductor - miaViz (development version)

miaViz

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

Microbiome Analysis Plotting and Visualization

Bioconductor version: Development (3.22)

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] ORCID: 0000-0002-8563-8884 , Felix G.M. Ernst [aut] ORCID: 0000-0001-5064-0928 , Leo Lahti [aut] ORCID: 0000-0001-5537-637X , Basil Courbayre [ctb], Giulio Benedetti [ctb] ORCID: 0000-0002-8732-7692 , Théotime Pralas [ctb], Chouaib Benchraka [ctb], Sam Hillman [ctb], Geraldson Muluh [ctb], Noah De Gunst [ctb], Ely Seraidarian [ctb], Himmi Lindgren [ctb], Akewak Jeba [ctb] ORCID: 0009-0007-1347-7552 , Vivian Ikeh [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 "4.5") 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")
Details biocViews Microbiome, Software, Visualization Version 1.17.9 In Bioconductor since BioC 3.13 (R-4.1) (4 years) License Artistic-2.0 | file LICENSE Depends R (>= 4.1.0), ggplot2, ggraph (>= 2.0), mia(>= 1.13.0), SummarizedExperiment, TreeSummarizedExperiment Imports ape, BiocGenerics, BiocParallel, DelayedArray, DirichletMultinomial, dplyr, ggnewscale, ggrepel, ggtree, methods, rlang, S4Vectors, scales, scater, SingleCellExperiment, stats, tibble, tidygraph, tidyr, tidytext, tidytree, viridis System Requirements URL https://github.com/microbiome/miaViz Bug Reports https://github.com/microbiome/miaViz/issues See More Suggests beeswarm, BiocStyle, bluster, circlize, ComplexHeatmap, ggh4x, knitr, patchwork, rmarkdown, shadowtext, testthat, vegan, vipor Linking To Enhances Depends On Me Imports Me iSEEtree Suggests Me HoloFoodR, MGnifyR, mia, miaSim Links To Me Build Report Build Report Package Archives

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

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