Designing synthetic bacterial communities for predictable plant phenotypes

add_condition | add condition |

All.filtered | Bacterial growth curves in 4 different media |

all_identical | Make sure all elements in list are identical |

block_effects | Estimate block main effects |

combine_datasets | Combine datasets |

dist2df | Distance to data.frame |

extract_taxonomy | Extract taxonomy info for one taxon |

homogenize_taxa | homogenize taxa in abundance matrix |

independent_lm_tests | Test all combinations of levels |

merge_phen_and_abun | Merge phenotype data with relative abundances of blocks |

metacoder_plot_go | Plot GO from edgeR |

metadata_from_rowname | Extract metadata from rownames |

mgsub | mgsub |

obtain_block_abundances | Obtain block abundances |

parse_tax_and_plot | Metacoder plot |

perm_binaryP_enrich | Permutation enrichment test of phosphate modulators |

plot_binary | Plot results from binary association |

plot_combined_effects | Plot heatmap of all effects |

plot_cross_mapping | Plot mapping id |

plotgg_heatmap_syncom_effects | Plot syncom effects |

plot_res | Plot binary association results |

plot_set | Plot the expression of a set of genes |

predict_from_main | Predict syncom from main effects |

read_mapsplit_dir | Read count tables from mapsplit dirs |

stat_smooth_func | Stat_smooth for coef of determination |

strain_rsqrd | Calculate R-squared |

term_class | From metacoder |

test_all_strains | Test all strains for change in phosphate accumulation |

test_auc | Test AUC |

test_single_block_phenptype | Test the effect of single block on phenotype |

test_single_community_phenotype | Test the effect of all single communities |

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