A Pipeline for Microbiome Analysis and Visualization

alpha_div | Alpha Diversity Calculations for tidy_micro |

bb_bars | Create stacked bar charts based on beta binomial model... |

bb_mods | Fit beta binomial models to each taxa within an OTU table |

beta_div | Beta Diversity Calculations for tidy_micro |

beta_heatmap | Create heatmaps of the supplied dissimilarity matrices |

bpd_cla | An OTU table of class level taxa counts from a BPD1 study |

bpd_clin | A data set containing the clinical data of the subjects... |

bpd_fam | An OTU table of family level taxa counts from BPD1 study |

bpd_ord | An OTU table of order level taxa counts study |

bpd_phy | An OTU table of phylum level taxa counts study |

cor_heatmap | Create correlation heatmaps of taxa and another continuous... |

cor_rocky_mtn | Create Rocky Mountain plots from taxa relative abundance... |

micro_alpha_reg | Linear regression on alpha diversities within a micro_set |

micro_chisq | Run Chi-Squared tests for each taxa |

micro_forest | Create forest plots from negative binomial taxa models |

micro_heatmap | Create heatmaps of estiamted coefficients from negative... |

micro_otu | Extract OTU table from tidyMicro set |

micro_pca | Calculate and plot principle components |

micro_PERMANOVA | A function to run PERMANOVA on tidi_micro data sets |

micro_rank_sum | Run rank sum tests for each taxa within an OTU table |

micro_rocky_mtn | Create Rocky Mountain plots from negative binomial taxa... |

mrsa_clin | A data set containing the clinical data of the subjects... |

mrsa_gen | An OTU table of genus level taxa counts from a MRSA study |

nb_bars | Create stacked bar charts based on negative binomial model... |

nb_mods | Fit negative binomial models to each taxa within an OTU table |

otu_filter | A function to aggregate low prevalence, abundance, or... |

pca_3d | Create 3d PCA plots |

pipe | Pipe operator |

ra_bars | Function to make stacked bar charts of taxa relative... |

taxa_boxplot | Function to make boxplots of taxa counts or relative... |

taxa_summary | Summarize the information |

three_mode | Create Three Mode PCA and PCoA plots |

tidyeval | Tidy eval helpers |

tidy_micro | A function to merge multiple OTU tables and clinical data... |

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