MicrobiotaProcess
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see MicrobiotaProcess.
an R package for analysis, visualization and biomarker discovery of microbiome
Bioconductor version: 3.11
MicrobiotaProcess is an R package for analysis, visualization and biomarker discovery of microbial datasets. It supports calculating alpha index and provides functions to visualize rarefaction curves. Moreover, it also supports visualizing the abundance of taxonomy of samples. And It also provides functions to perform the PCA, PCoA and hierarchical cluster analysis. In addition, MicrobiotaProcess also provides a method for the biomarker discovery of metagenome or other datasets.
Author: Shuangbin Xu [aut, cre] 
, Guangchuang Yu [aut, ctb]
Maintainer: Shuangbin Xu <xshuangbin at 163.com>
citation("MicrobiotaProcess")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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")| MicrobiotaProcess: basics analysis using MicrobiotaProcess. | HTML | R Script |
| MicrobiotaProcess: biomarker discovery using MicrobiotaProcess. | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | FeatureExtraction, Microbiome, MultipleComparison, Software, Visualization |
| Version | 1.0.5 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4 years) |
| License | GPL (>= 3.0) |
| Depends | R (>= 4.0.0) |
| Imports | ape, plyr, tidyr, ggplot2, phyloseq, magrittr, dplyr, Biostrings, ggrepel, vegan, rentrez, reshape, zoo, ggtree, tidytree, gtools, MASS, methods, randomForest, rlang, tibble, grDevices, stats, utils, coin, ggsignif, scales, Rmisc, DECIPHER, biomformat, yaml, phangorn, patchwork |
| System Requirements | |
| URL | https://github.com/YuLab-SMU/MicrobiotaProcess/ |
| Bug Reports | https://github.com/YuLab-SMU/MicrobiotaProcess/issues |
See More
| Suggests | DT, prettydoc, treeio, tidyverse, testthat, knitr, nlme |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MicrobiotaProcess_1.0.5.tar.gz |
| Windows Binary | MicrobiotaProcess_1.0.5.zip |
| macOS 10.13 (High Sierra) | MicrobiotaProcess_1.0.5.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 |
| Old Source Packages for BioC 3.11 | Source Archive |