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MicrobiotaProcess R Package

repository·master·Indexed 41 days ago

https://github.com/yulab-smu/microbiotaprocess

An R package for managing and analyzing microbiome and ecological data. It utilizes the Microbiota Process Sequencing Experiment (MPSE) structure to integrate primary and intermediate datasets within a tidy framework for downstream analysis and visualization.

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What's inside MicrobiotaProcess

  1. What is an MPSE?

    master
    An MPSE (Microbiota Process Sequencing Experiment) is the core data structure in MicrobiotaProcess. It is designed to integrate both primary microbiome datasets (like OTU/ASV tables) and intermediate/downstream datasets (like metadata, phylogenetic trees, or functional annotations) into a single, unified object. This structure allows for efficient exploration and analysis within a tidy framework.

  2. Install MicrobiotaProcess

    master

    You can install the released version of MicrobiotaProcess via Bioconductor or the development version via GitHub.

    Install via Bioconductor (Recommended)

    Use BiocManager to install the stable release.

    Install via GitHub (Development Version)

    Use the remotes package to install the latest development version directly from the YuLab-SMU/MicrobiotaProcess repository.

    ## Install via Bioconductor
if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
# BiocManager::install("BiocUpgrade") ## you may need this
BiocManager::install("MicrobiotaProcess")

## Install via GitHub
if (!requireNamespace("remotes", quietly=TRUE))
    install.packages("remotes")
remotes::install_github("YuLab-SMU/MicrobiotaProcess")