In HuaZou/MicrobiomeAnalysis: Data analysis toolkits in metagenomics

MicrobiomeAnalysis: A comprehensive R package for managing and analyzing microbiome data

Biocpkg <- function (pkg) {
    sprintf("[%s](http://bioconductor.org/packages/%s)", pkg, pkg)
}
library(conflicted)
conflicted::conflict_prefer("filter", "dplyr")
knitr::opts_chunk$set(fig.path = "inst/figures/README-")

This package has many unique features:

The Overview of MicrobiomeAnalysis

knitr::include_graphics("./man/figures/Schematic.png")

:writing_hand: Authors

Hua Zou

:arrow_double_down: Installation

Requiring the R-base version more than 4.1.0. Some of the dependencies from CRAN or bioconductor, but others, are only obtained from github. the version of dependencies are as follows:

dependencies in CRAN & Bioconductor

install.packages("pacman")

library(pacman)

pacman::p_load(phyloseq, dplyr, tibble, Biobase, ggplot2)

dependencies in github

# Step 1: Install devtools
if (!requireNamespace(c("remotes", "devtools"), quietly=TRUE)) {
  install.packages(c("devtools", "remotes"))
}
library(devtools)
#library(remotes)

# Step 2: install corncob package
devtools::install_github("bryandmartin/corncob")
# remotes::install_github("bryandmartin/corncob")

Installing MicrobiomeAnalysis

Get the released MicrobiomeAnalysis packages from here.

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

the development version from github:

devtools::install_github("HuaZou/MicrobiomeAnalysis", 
                         dependencies = c("Depends", "Imports", "LinkingTo"),
                         repos = c("https://cloud.r-project.org/",
                                   BiocManager::repositories()))

• specific version

devtools::install_github("HuaZou/MicrobiomeAnalysis@v1.0.3", 
                         dependencies = c("Depends", "Imports", "LinkingTo"),
                         repos = c("https://cloud.r-project.org/",
                                   BiocManager::repositories()))

• specific branch

devtools::install_github("HuaZou/MicrobiomeAnalysis", 
                         dependencies = c("Depends", "Imports", "LinkingTo"),
                         repos = c("https://cloud.r-project.org/",
                                   BiocManager::repositories()),
                         ref = "dev")

:book: Vignette

Using the following command and Choosing the html for more details.

utils::browseVignettes(package="MicrobiomeAnalysis")

the tutorial of Microbiota Data Analysis by MicrobiomeAnalysis made by bookdown.

:sparkling_heart: Contributing

Welcome any contributions or comments, and you can file them here.

:trophy: Acknowledgement

Thanks all the developers of the methods integrated into MicrobiomeAnalysis. The reference package is microbiomeMarker. The R codes of differential analysis methods are almost from microbiomeMarker.

:eight_pointed_black_star: Citation

Kindly cite by using citation("MicrobiomeAnalysis") if you think MicrobiomeAnalysis helps you. Alternative way is Zou H (2022). MicrobiomeAnalysis: An R package for analysis and visualization in metagenomics. R package version 1.0.3, .

HuaZou/MicrobiomeAnalysis documentation built on May 13, 2024, 11:10 a.m.