MicrobiotaProcess
This is the released version of MicrobiotaProcess; for the devel version, see MicrobiotaProcess.
A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework
Bioconductor version: Release (3.23)
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>
citation("MicrobiotaProcess")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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")| Introduction to MicrobiotaProcess | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | FeatureExtraction, Microbiome, MultipleComparison, Software, Visualization |
| Version | 1.24.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 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, ggalluvial (>= 0.11.1), forcats, phyloseq, aplot, ggnewscale, ggside, ggh4x, hopach, parallel, shadowtext, DirichletMultinomial, ggpp, BiocManager, rhdf5 |
| 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_1.24.0.tar.gz |
| Windows Binary (x86_64) | MicrobiotaProcess_1.24.0.zip |
| macOS Binary (big-sur-x86_64) | MicrobiotaProcess_1.24.0.tgz |
| macOS Binary (sonoma-arm64) | MicrobiotaProcess_1.24.0.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 |