Function reference • miso

All functions
`ERR260132`	Precomputed lineage calling and coverage example.
`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.
`bracken_to_phyloseq()`	Converts BRACKEN results to a phyloseq object.
`build_lineage()`	Build the lineage from a SILVA path string.
`combinatorial_association()`	Run differential association tests between between all combinations of a factor variable with DESeq2. Can be used as post-hoc test for regression.
`config_association()`	Build a configuration for the alignment workflows.
`config_chimera()`	Build a configuration for chimera removal.
`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_layout()`	Build a configuration for the plate layout.
`config_power()`	Build a configuration for power analysis.
`config_preprocess()`	Build a configuration for raw read preprocessing.
`config_reference()`	Build a configuration for the reference removal 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.
`download_sra()`	Download data from SRA.
`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.
`file_formats`	Presets for read file formats.
`filter_counts()`	Filter low presence taxa from a count matrix.
`filter_reference()`	Filter a set of reference sequences from the data set.seed
`find_alignments()`	Find alignment BAM files in a given directory.
`find_read_files()`	Find read files in a given directory.
`find_taxa()`	Checks whether taxa from one taxonomy table are contained in another table.
`layout()`	Generate a plate layout from a sample manifest.
`merge_transcripts()`	Merge transcripts into a single database
`miso-package` `miso`	miso.
`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_bb_fits()`	Plot the Betabinomial fits for all taxa in a phyloseq object
`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.
`power_analysis()`	Run a power analysis for microbe abundances from a reference sample.
`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.
`reads_to_phyloseq()`	Converts read count data to a phyloseq object.
`remove_chimeras()`	Removes chimeric reads from amplicon sequencing data.
`remove_reference()`	Removes sequence that map to a given reference.
`select()`	Very simple select for miso artifacts. Just gets a particular entry.
`silva_build_taxonomy()`	Build the lineages for the entire SILVA database.
`sra_presets`	The available presets for SRA submissions. They all map to MIMARKS or MIMS packages
`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.

Reference

All functions