Man pages for microbial
Do 16s Data Analysis and Generate Figures

betadivcalcaute beta diversity
betatestPERMANOVA test for phyloseq
biomarkerIdentify biomarker by using randomForest method
buildTreecontruction of plylogenetic tree (extreme slow)
data-physeqThe physeq data was modified from the (Data) Global patterns...
difftestCalculate differential bacteria with DESeq2
distcolordistinguish colors for making figures
do_aovdo anova test and return results as data.frame
dot-checkfilecheck file format
dot-getstarreplace p value with star
dot-lda.funLEfse function
do_ttestdo t.test
do_wilcoxdo wilcox test
glmrDo the generalized linear model regression
ldamarkerIdentify biomarker by using LEfSe method
lightcolorlight colors for making figures
normalizeNormalize the phyloseq object with different methods
otu_tableextract otu table
phy_treeRetrieve phylogenetic tree (phylo-class) from object.
plotalphaplot alpha diversity
plotbarplot bar for relative abundance for bacteria
plotbetaplot beta diversity
plotdiffplot differential results
plotLDAplot LEfSe results from ldamarker function
plotmarkerplot the biomarker from the biomarker function with...
plotqualityplot the quality for the fastq file
prefilterfilter the phyloseq
preRefDownload the reference database
processSeqPerform dada2 analysis
psmeltMelt phyloseq data object into large data.frame
richnesscalculat the richness for the phyloseq object
sample_dataextract sample information
subset_samplesSubset the phyloseq based on sample
subset_taxaSubset species by taxonomic expression
tax_tableextract taxonomy table
microbial documentation built on Nov. 1, 2021, 5:08 p.m.