MARco

MARco is an R code and function set for microbiome analysis with less pain to generate basic plots of microbial ecology, including alpha diversity boxplots, violin plots, beta diversity ordination (PCoA based on Bray-Curtis dissimilarity) with ADONIS test, and several statistical and visualization tools (see below). MARco also contains several discrete color sets for applying to your grouped plots. For advanced analysis, co-occurrence network analysis is also able to conduct by MARco.

Tutorial and all updated codes will be released on http://www.lifescipy.net/MARco/MARco.html.

Please cites:
Liu, P.-Y. poyuliu/MARco: MARco: Microbiome Analysis RcodeDB (Version v1.0). Zenodo. Available online: http://doi.org/10.5281/zenodo.4589897 (accessed on Day Month Year).

Required packages:

vegan with functions for most community ecology analyses
fossil for calculating Chao1 index
vioplot for ploting violin plots
igraph for constructing network
SpiecEasi for calculating SparCC correlation, how to install: https://github.com/zdk123/SpiecEasi
DESeq2 RNA-Seq based differential expression test, see details on Bioconductor: https://bioconductor.org/packages/release/bioc/html/DESeq2.html
pheatmap for plot heatmap
MASS for LDA (linear discriminant analysis) effect size (LEfSe)
gage for GAGE (Generally Applicable Gene-set Enrichment) analysis
cluster and clusterSim for Enterotyping
randomForest, plyr, rfUtilities, caret, ROCR and pROC for Random Forest analysis
doParallel for Windows version Random Forest analysis (runRFwin())

Available codes & how to use:

1. Microbiome analysis function set
2. color sets
3. network analysis function modules
4. Random Forest function modules
5. Enterotyping
6. Reformat KEGG Orthology (KO) to pathways and modules from metagenome, metatranscriptome, or functional prediction data

install dependencies from Bioconductor

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install(c("gage","DESeq2"))

install dependencies from GitHub

library(devtools)
install_github("zdk123/SpiecEasi")

if fail to install rgl package automatically
please refer to: https://r-forge.r-project.org/R/?group_id=234

 install.packages("rgl", repos="http://R-Forge.R-project.org")

install package from github:

library(devtools)
install_github("poyuliu/MARco")

sourcing MARco R library

library(MARco)