All functions

ERR260132

Precomputed lineage calling and coverage example.

align_long_reads()

Align long reads (for instance from nanopore sequencing) to a reference database.

align_short_reads()

Aligns metagenomic shotgun reads against a reference.

annotate_contigs()

Annotate diamond database hits with transcript info.

annotate_silva()

Annotate the sequences in the SILVA database file.

as.matrix(<mbquant>)

Convert a mbquant data table to a matrix.

as_phyloseq()

Converts the denoise artifact to a phyloseq object.

association()

Run differential association tests between taxa counts and exogenous factors.

build_lineage()

Build the lineage from a SILVA path string.

combinatorial_association()

Run differential association tests between between all combinations of a factor variable. Can be used as post-hoc test for regression.

config_align()

Build a configuration for the alignment workflows.

config_association()

Build a configuration for the alignment workflows.

config_count()

Build a configuration for the transcript counting workflow.

config_demultiplex()

Build a configuration for the demultiplexing workflow.

config_denoise()

Build a configuration for the DADA2 workflow.

config_preprocess()

Build a configuration for raw read preprocessing.

config_reference()

Build a configuration for the reference removal workflow.

config_rep()

Build a configuration for the rate workflow.

config_slimm()

Build a configuration for the SLIMM workflow.

config_sra()

Build a configuration for the SRA submission workflow.

count_references()

Count alignment hits to a reference database.

demultiplex()

Splits FASTQ files into individual samples.

denoise()

Runs a full DADA2 workflow.

discretize()

Discretize all continuous variables in a data frame.

download_bacterial_transcripts()

Download the entire ENSEMBL transcript DB for bacteria.

download_files()

Download a list of files.

effective_lengths()

Calculate the effective transcript lengths. This is the mean number of positions in the transcript the fragment could map to.

em_count()

Count transcripts using an Expectation Maximization (EM) algorithm.

filter_counts()

Filter low presence taxa from a count matrix.

filter_reference()

Filter a set of reference sequences from the data set.seed

find_read_files()

Find read files in a given directory.

find_taxa()

Checks whether taxa from one taxonomy table are contained in another table.

mbtools

mbtools.

merge_transcripts()

Merge transcripts into a single database

mock_plot()

Creates a plot of measured taxa quantifications vs. reference quantification.

mockrobiota()

Downloads a complete data set from mockrobiota.

mothur_to_dada()

Converts taxa annotations from mothur format to dada2 format.

normalize()

Normalize a set of read counts across samples

orlitsky()

Orlitsky's diminishing attenuation estimator (q2/3).

parse_ensembl_id()

Parse annotations from an ENSEMBL id

plot_counts()

Plots counts for several taxa across a co-variable

plot_entropy()

Plots the distribution of base entropy for each cycle.

plot_lengths()

Plots the distribution of sequence lengths with acceptable quality.

plot_qualities()

Plots the quality profile for an entire experiment.

plot_taxa()

Plots relative distribution for taxa across samples.

preprocess()

Runs preprocessing of sequencing reads.

quality_control()

Workflow for basic quality assessment of the read files.

quality_profile()

Get the quality profiles and base calls for each cycle across all input files.

read_bam()

Read alignments from a BAM file.

read_blast()

Read a blast hit/alignment file.

read_length()

Heuristic to get the median read length from a BAM file.access

read_slimm()

Reads SLIMM output to a data table.

read_slimm_coverage()

Reads SLIMM coverage to a data table.

remove_reference()

Removes sequence that map to a given reference.

replication_rates()

Estimate replication rates by the iRep method.

select()

Very simple select for mbtools artifacts. Just gets a particular entry.

silva_build_taxonomy()

Build the lineages for the entire SILVA database.

slimm()

Quantifies abundances and coverage using SLIMM.

slimm_files

The SLIMM taxonomy databases

sra_files()

List samples and read files in a directory.

sra_submission()

Prepare submission files for the NCBI sequence read archive (SRA).

standardize()

Standardize all continuous columns of a data frame.

taxa_count()

Counts the reads for a specific taxonomy level.

taxa_metrics()

Calculates what percentage of taxa was found in a reference set.

taxa_quants()

Compares taxa quantification from a measurement to a reference ground truth.

types()

Applies the specified types to a data frame-like object.

with_classification()

Quantify classification rates for each taxonomic rank.