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MicrobiotaProcess
This is thereleased version of MicrobiotaProcess; for the devel version, seeMicrobiotaProcess.
A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework
Bioconductor version: Release (3.22)
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: 0000-0003-3513-5362, Guangchuang Yu [aut, ctb] ORCID: 0000-0002-6485-8781
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")BiocManager::install("MicrobiotaProcess")For older versions of R, please refer to the appropriateBioconductor 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 | 1.22.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (5.5 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | MicrobiotaProcess_1.22.0.tar.gz |
| Windows Binary (x86_64) | MicrobiotaProcess_1.22.0.zip |
| macOS Binary (x86_64) | MicrobiotaProcess_1.22.0.tgz |
| macOS Binary (arm64) | MicrobiotaProcess_1.22.0.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 |
| Old Source Packages for BioC 3.22 | Source Archive |