High Throughput Sequencing of Stable Isotope Probing Data Analysis

as.Num | conversion to numeric |

BD_shift | Assessing the magnitude of BD shifts with 16S rRNA community... |

calc_atom_excess | Calculate atom fraction excess |

calc_Gi | Calculate G+C from unlabeled buoyant density |

calc_Mheavymax | Calculate the theoretical maximum molecular weight of... |

data-physeq_rep3 | (Data) A simulated HTS-SIP dataset |

data-physeq_rep3_qPCR | (Data) qPCR data associated with the physeq_rep3 HTS-SIP... |

data-physeq_S2D1 | (Data) A subset of full HTS-SIP dataset (Substrates=2,... |

data-physeq_S2D1_l | (Data) A subset of full HTS-SIP dataset (Substrates=2,... |

data-physeq_S2D2 | (Data) A subset of full HTS-SIP dataset (Substrates=2,... |

data-physeq_S2D2_l | (Data) A subset of full HTS-SIP dataset (Substrates=2,... |

delta_BD | delta_BD calculation |

DESeq2_l2fc | Calculating log2 fold change for HTS-SIP data. |

evaluate_matches | Evaluate String Interpolation Matches |

expr_param_extract | Extract all quoted values in the expression used for phyloseq... |

extract_expressions | Extract Expression Objects from String Interpolation Matches |

extract_formats | Extract String Interpolation Formats from Matched... |

filter_l2fc | Filter l2fc table |

format_metadata | Format phyloseq metadata for calculating BD range overlaps. |

fraction_overlap | Calculate the BD range overlap of gradient fractions |

get_treatment_params | Get parameters for subsetting the phyloseq dataset |

gradient_sim | Simulate HTS-SIP communities for 1 density gradient |

heavy_SIP | Heavy-SIP analysis |

HRSIP | (MW-)HR-SIP analysis |

HTSSIP | HTSSIP: analyzing high throughput sequence data from... |

HTSSIP_sim | Simulate a HTS-SIP dataset |

match_brace | Utility Function for Matching a Closing Brace |

match_placeholders | Match Expression Placeholders for String Interpolation |

max_BD_range | Adjusting BD range size if negative. |

OTU_qPCR_trans | Transform OTU counts based on qPCR data |

overlap_wmean_dist | Calculating weighted mean beta-diversities of overlapping... |

parse_dist | Filtering out non-relevant distances in distance matrix |

perc_overlap | Calculate the percent overlap between two ranges (x & y). |

phyloseq2df | phyloseq data object conversion to data.frame |

phyloseq2table | Phyloseq conversion to a ggplot-formatted table |

phyloseq_list_ord_dfs | Converting ordination objects to data.frames |

phyloseq_ord_plot | Plotting beta diversity ordination |

phyloseq_subset | Make a list of phyloseq object subsets |

physeq_format | Checking format of phyloseq object for HTSSIP compatibility |

physeq_list_betaDiv | calculating beta diversity for a list of phyloseq objects |

physeq_list_ord | calculating ordinations from a list of distance matrices |

qPCR_sim | Simulate qPCR values |

qSIP_atom_excess | Calculate atom fraction excess using q-SIP method |

qSIP_atom_excess_format | Reformat a phyloseq object of qSIP_atom_excess analysis |

qSIP_bootstrap | Calculate bootstrap CI for atom fraction excess using q-SIP... |

SIP_betaDiv_ord | Calculating & plotting beta diversity for a list of phyloseq... |

stringterpolate | String Interpolation |

tss | Total sum scaling |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.