DOI: 10.18129/B9.bioc.MicrobiotaProcess  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see MicrobiotaProcess.

A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

Bioconductor version: 3.16

MicrobiotaProcess is an R package for analysis, visualization and biomarker discovery of microbial datasets. It introduces MPSE class, this make it more interoperable with the existing computing ecosystem. Moreover, it introduces a tidy microbiome data structure paradigm and analysis grammar. It provides a wide variety of microbiome data analysis procedures under the unified and common framework (tidy-like framework).

Author: Shuangbin Xu [aut, cre] , Guangchuang Yu [aut, ctb]

Maintainer: Shuangbin Xu <xshuangbin at 163.com>

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biocViews FeatureExtraction, Microbiome, MultipleComparison, Software, Visualization
Version 1.10.3
In Bioconductor since BioC 3.11 (R-4.0) (3 years)
License GPL (>= 3.0)
Depends R (>= 4.0.0)
Imports ape, tidyr, ggplot2, magrittr, dplyr, Biostrings, ggrepel, vegan, zoo, ggtree, tidytree (>= 0.4.2), MASS, methods, rlang, tibble, grDevices, stats, utils, coin, ggsignif, patchwork, ggstar, tidyselect, SummarizedExperiment, foreach, treeio(>= 1.17.2), pillar, cli, plyr, dtplyr, ggtreeExtra, data.table
Suggests rmarkdown, prettydoc, testthat, knitr, nlme, phangorn, DECIPHER, randomForest, jsonlite, biomformat, scales, yaml, withr, S4Vectors, purrr, seqmagick, glue, corrr, ggupset, ggVennDiagram, gghalves, ggalluvial (>= 0.11.1), forcats, phyloseq, aplot, ggnewscale, ggside, ggh4x, hopach, parallel, shadowtext, DirichletMultinomial
URL https://github.com/YuLab-SMU/MicrobiotaProcess/
BugReports https://github.com/YuLab-SMU/MicrobiotaProcess/issues
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