Chapter 2 How to install MicrobiomeAnalysis

Before installation, you should install the two following software.

• R 4.1.2 (R Core Team 2021) or later release Download link.

• Rstudio Desktop Download link.

2.1 Installation

First, installing either R package devtools or remotes:

if (!requireNamespace(c("devtools", "remotes"), quietly = TRUE)) {
  install.packages(c("devtools", "remotes"))
}

devtools::install_github("HuaZou/MicrobiomeAnalysis")
# remotes::install_github("HuaZou/MicrobiomeAnalysis")

# specific release
devtools::install_github("HuaZou/MicrobiomeAnalysis@release-v1.0.3")

Alternatively, you can install the latest released package from releases:

install.packages("MicrobiomeAnalysis*.tar.gz", repos = NULL, type = "source")

The MicrobiomeAnalysis package took dplyr, phyloseq, purrr, magrittr, tibble, metagenomeSeq, biomformat, SummarizedExperiment, ggplot2 and caret etc as directly import packages.

2.2 Vignette

For brief introduction to use MicrobiomeAnalysis, please refer to vignette and choose html format to do a practice.

utils::browseVignettes(package="MicrobiomeAnalysis")

2.3 Authors

• Hua Zou

References

R Core Team. 2021. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. https://www.R-project.org/.