All functions
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align_bowtie2()
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Aligns metagenomic shotgun sample against a reference |
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as.matrix(<mbquant>)
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Convert a mbquant data table to a matrix. |
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association()
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Run differential association tests between taxa counts and exogenous
factors. |
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combinatorial_association()
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Run differential association tests between between all combinations of a
factor variable. Can be used as post-hoc test for regression. |
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discretize()
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Discretize all continuous variables in a data frame. |
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download_index()
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Builds index files for human sequence identification |
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find_taxa()
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Checks whether taxa from one taxonomy table are contained in another table. |
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mbtools
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mbtools. |
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mock_plot()
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Creates a plot of measured taxa quantifications vs. reference quantification. |
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mockrobiota()
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Downloads a complete data set from mockrobiota. |
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mothur_to_dada()
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Converts taxa annotations from mothur format to dada2 format. |
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normalize()
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Normalize a set of read counts across samples |
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orlitsky()
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Orlitsky's diminishing attenuation estimator (q2/3). |
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plot_counts()
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Plots counts for several taxa across a co-variable |
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plot_taxa()
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Plots relative distribution for taxa across samples. |
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read_slimm()
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Reads SLIMM output to a data table. |
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remove_organism()
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Removes sequence contamination from another target organism (for instance
human sequences). |
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run_slimm()
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Quantifies abundances for the bacteria using SLIMM |
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split_barcodes()
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Splits FASTQ files into individual samples. |
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sra_files()
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List samples and read files in a directory. |
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standardize()
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Standardize all continuous columns of a data frame. |
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taxa_count()
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Counts the reads for a specific taxonomy level. |
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taxa_metrics()
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Calculates what percentage of taxa was found in a reference set. |
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taxa_quants()
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Compares taxa quantification from a measurement to a reference ground truth. |
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types()
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Applies the specified types to a data frame-like object. |