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 |

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