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Bioconductor - miaViz

miaViz

This is the released version of miaViz; for the devel version, see miaViz.

Microbiome Analysis Plotting and Visualization

Bioconductor version: Release (3.21)

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], Nitesh Turaga [ctb], Chouaib Benchraka [ctb], Sam Hillman [ctb], Muluh Muluh [ctb], Noah De Gunst [ctb], Ely Seraidarian [ctb], Himmi Lindgren [ctb], 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")

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 1.16.0 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 BiocStyle, bluster, circlize, ComplexHeatmap, ggh4x, knitr, patchwork, rmarkdown, shadowtext, testthat, vegan 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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