Man pages for microbial
Do 16s Data Analysis and Generate Figures
| betadiv | calcaute beta diversity |
| betatest | PERMANOVA test for phyloseq |
| biomarker | Identify biomarker by using randomForest method |
| buildTree | contruction of plylogenetic tree (extreme slow) |
| data-physeq | The physeq data was modified from the (Data) Global patterns... |
| difftest | Calculate differential bacteria with DESeq2 |
| distcolor | distinguish colors for making figures |
| do_aov | do anova test and return results as data.frame |
| dot-checkfile | check file format |
| dot-getstar | replace p value with star |
| dot-lda.fun | LEfse function |
| do_ttest | do t.test |
| do_wilcox | do wilcox test |
| glmr | Do the generalized linear model regression |
| ldamarker | Identify biomarker by using LEfSe method |
| lightcolor | light colors for making figures |
| normalize | Normalize the phyloseq object with different methods |
| otu_table | extract otu table |
| phy_tree | Retrieve phylogenetic tree (phylo-class) from object. |
| plotalpha | plot alpha diversity |
| plotbar | plot bar for relative abundance for bacteria |
| plotbeta | plot beta diversity |
| plotdiff | plot differential results |
| plotLDA | plot LEfSe results from ldamarker function |
| plotmarker | plot the biomarker from the biomarker function with... |
| plotquality | plot the quality for the fastq file |
| prefilter | filter the phyloseq |
| preRef | Download the reference database |
| processSeq | Perform dada2 analysis |
| psmelt | Melt phyloseq data object into large data.frame |
| richness | calculat the richness for the phyloseq object |
| sample_data | extract sample information |
| subset_samples | Subset the phyloseq based on sample |
| subset_taxa | Subset species by taxonomic expression |
| tax_table | extract taxonomy table |
