MicrobiotaProcess
This is the development version of MicrobiotaProcess; for the stable release version, see MicrobiotaProcess.
A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Shuangbin Xu <xshuangbin at 163.com>
citation("MicrobiotaProcess")):
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("MicrobiotaProcess")
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("MicrobiotaProcess")| Introduction to MicrobiotaProcess | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | FeatureExtraction, Microbiome, MultipleComparison, Software, Visualization |
| Version | 1.19.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4.5 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, ggfun (>= 0.1.1) |
| System Requirements | |
| URL | https://github.com/YuLab-SMU/MicrobiotaProcess/ |
| Bug Reports | https://github.com/YuLab-SMU/MicrobiotaProcess/issues |
See More
| Suggests | rmarkdown, prettydoc, testthat, knitr, nlme, phangorn, DECIPHER, randomForest, jsonlite, biomformat, scales, yaml, withr, S4Vectors, purrr, seqmagick, glue, ggupset, ggVennDiagram, gghalves, ggalluvial (>= 0.11.1), forcats, phyloseq, aplot, ggnewscale, ggside, ggh4x, hopach, parallel, shadowtext, DirichletMultinomial, ggpp, BiocManager |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | parafac4microbiome |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MicrobiotaProcess_1.19.0.tar.gz |
| Windows Binary (x86_64) | MicrobiotaProcess_1.19.0.zip (64-bit only) |
| macOS Binary (x86_64) | MicrobiotaProcess_1.19.0.tgz |
| macOS Binary (arm64) | MicrobiotaProcess_1.19.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MicrobiotaProcess |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MicrobiotaProcess |
| Bioc Package Browser | https://code.bioconductor.org/browse/MicrobiotaProcess/ |
| Package Short Url | https://bioconductor.org/packages/MicrobiotaProcess/ |
| Package Downloads Report | Download Stats |