Do 16s Data Analysis and Generate Figures
calcaute beta diversity
PERMANOVA test for phyloseq
Identify biomarker by using randomForest method
contruction of plylogenetic tree (extreme slow)
The physeq data was modified from the (Data) Global patterns of 16S rR...
Calculate differential bacteria with DESeq2
distinguish colors for making figures
do anova test and return results as data.frame
do t.test
do wilcox test
check file format
replace p value with star
LEfse function
Do the generalized linear model regression
Identify biomarker by using LEfSe method
light colors for making figures
Normalize the phyloseq object with different methods
extract otu table
Retrieve phylogenetic tree (phylo-class) from object.
plot alpha diversity
plot bar for relative abundance for bacteria
plot beta diversity
plot differential results
plot LEfSe results from ldamarker function
plot the biomarker from the biomarker function with randomForest
plot the quality for the fastq file
filter the phyloseq
Download the reference database
Perform dada2 analysis
Melt phyloseq data object into large data.frame
calculat the richness for the phyloseq object
extract sample information
Subset the phyloseq based on sample
Subset species by taxonomic expression
extract taxonomy table
Provides functions to enhance the available statistical analysis procedures in R by providing simple functions to analysis and visualize the 16S rRNA data.Here we present a tutorial with minimum working examples to demonstrate usage and dependencies.