All functions
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ERR260132
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Precomputed lineage calling and coverage example. |
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align_long_reads()
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Align long reads (for instance from nanopore sequencing) to a reference
database. |
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align_short_reads()
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Aligns metagenomic shotgun reads against a reference. |
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annotate_contigs()
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Annotate diamond database hits with transcript info. |
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annotate_silva()
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Annotate the sequences in the SILVA database file. |
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as.matrix(<mbquant>)
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Convert a mbquant data table to a matrix. |
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as_phyloseq()
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Converts the denoise artifact to a phyloseq object. |
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association()
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Run differential association tests between taxa counts and exogenous
factors. |
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build_lineage()
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Build the lineage from a SILVA path string. |
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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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config_align()
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Build a configuration for the alignment workflows. |
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config_association()
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Build a configuration for the alignment workflows. |
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config_count()
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Build a configuration for the transcript counting workflow. |
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config_demultiplex()
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Build a configuration for the demultiplexing workflow. |
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config_denoise()
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Build a configuration for the DADA2 workflow. |
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config_preprocess()
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Build a configuration for raw read preprocessing. |
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config_reference()
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Build a configuration for the reference removal workflow. |
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config_rep()
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Build a configuration for the rate workflow. |
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config_slimm()
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Build a configuration for the SLIMM workflow. |
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config_sra()
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Build a configuration for the SRA submission workflow. |
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count_references()
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Count alignment hits to a reference database. |
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demultiplex()
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Splits FASTQ files into individual samples. |
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denoise()
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Runs a full DADA2 workflow. |
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discretize()
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Discretize all continuous variables in a data frame. |
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download_bacterial_transcripts()
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Download the entire ENSEMBL transcript DB for bacteria. |
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download_files()
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Download a list of files. |
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effective_lengths()
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Calculate the effective transcript lengths. This is the mean number of
positions in the transcript the fragment could map to. |
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em_count()
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Count transcripts using an Expectation Maximization (EM) algorithm. |
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filter_counts()
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Filter low presence taxa from a count matrix. |
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filter_reference()
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Filter a set of reference sequences from the data set.seed |
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find_read_files()
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Find read files in a given directory. |
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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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merge_transcripts()
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Merge transcripts into a single database |
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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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parse_ensembl_id()
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Parse annotations from an ENSEMBL id |
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plot_counts()
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Plots counts for several taxa across a co-variable |
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plot_entropy()
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Plots the distribution of base entropy for each cycle. |
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plot_lengths()
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Plots the distribution of sequence lengths with acceptable quality. |
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plot_qualities()
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Plots the quality profile for an entire experiment. |
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plot_taxa()
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Plots relative distribution for taxa across samples. |
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preprocess()
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Runs preprocessing of sequencing reads. |
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quality_control()
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Workflow for basic quality assessment of the read files. |
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quality_profile()
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Get the quality profiles and base calls for each cycle across all
input files. |
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read_bam()
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Read alignments from a BAM file. |
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read_blast()
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Read a blast hit/alignment file. |
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read_length()
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Heuristic to get the median read length from a BAM file.access |
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read_slimm()
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Reads SLIMM output to a data table. |
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read_slimm_coverage()
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Reads SLIMM coverage to a data table. |
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remove_reference()
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Removes sequence that map to a given reference. |
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replication_rates()
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Estimate replication rates by the iRep method. |
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select()
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Very simple select for mbtools artifacts. Just gets a particular entry. |
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silva_build_taxonomy()
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Build the lineages for the entire SILVA database. |
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slimm()
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Quantifies abundances and coverage using SLIMM. |
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slimm_files
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The SLIMM taxonomy databases |
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sra_files()
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List samples and read files in a directory. |
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sra_submission()
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Prepare submission files for the NCBI sequence read archive (SRA). |
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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. |
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with_classification()
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Quantify classification rates for each taxonomic rank. |