Man pages for Gibbons-Lab/mbtools
Provides helper functions for microbiome preprocessing and analysis

align_long_readsAlign long reads (for instance from nanopore sequencing) to a...
align_short_readsAligns metagenomic shotgun reads against a reference.
annotate_contigsAnnotate diamond database hits with transcript info.
annotate_silvaAnnotate the sequences in the SILVA database file.
as.matrix.mbquantConvert a mbquant data table to a matrix.
as_phyloseqConverts the denoise artifact to a phyloseq object.
associationRun differential association tests between taxa counts and...
build_lineageBuild the lineage from a SILVA path string.
combinatorial_associationRun differential association tests between between all...
config_alignBuild a configuration for the alignment workflows.
config_associationBuild a configuration for the alignment workflows.
config_countBuild a configuration for the transcript counting workflow.
config_demultiplexBuild a configuration for the demultiplexing workflow.
config_denoiseBuild a configuration for the DADA2 workflow.
config_powerBuild a configuration for power analysis.
config_preprocessBuild a configuration for raw read preprocessing.
config_referenceBuild a configuration for the reference removal workflow.
config_repBuild a configuration for the rate workflow.
config_slimmBuild a configuration for the SLIMM workflow.
config_sraBuild a configuration for the SRA submission workflow.
count_referencesCount alignment hits to a reference database.
demultiplexSplits FASTQ files into individual samples.
denoiseRuns a full DADA2 workflow.
discretizeDiscretize all continuous variables in a data frame.
download_bacterial_transcriptsDownload the entire ENSEMBL transcript DB for bacteria.
download_filesDownload a list of files.
effective_lengthsCalculate the effective transcript lengths. This is the mean...
em_countCount transcripts using an Expectation Maximization (EM)...
ERR260132Precomputed lineage calling and coverage example.
filter_countsFilter low presence taxa from a count matrix.
filter_referenceFilter a set of reference sequences from the data set.seed
find_read_filesFind read files in a given directory.
find_taxaChecks whether taxa from one taxonomy table are contained in...
merge_transcriptsMerge transcripts into a single database
mock_plotCreates a plot of measured taxa quantifications vs. reference...
mockrobiotaDownloads a complete data set from mockrobiota.
mothur_to_dadaConverts taxa annotations from mothur format to dada2 format.
normalizeNormalize a set of read counts across samples
orlitskyOrlitsky's diminishing attenuation estimator (q2/3).
parse_ensembl_idParse annotations from an ENSEMBL id
plot_countsPlots counts for several taxa across a co-variable
plot_entropyPlots the distribution of base entropy for each cycle.
plot_lengthsPlots the distribution of sequence lengths with acceptable...
plot_qualitiesPlots the quality profile for an entire experiment.
plot_taxaPlots relative distribution for taxa across samples.
power_analysisRun a power analysis for microbe abundances from a reference...
preprocessRuns preprocessing of sequencing reads.
quality_controlWorkflow for basic quality assessment of the read files.
quality_profileGet the quality profiles and base calls for each cycle across...
read_bamRead alignments from a BAM file.
read_blastRead a blast hit/alignment file.
read_lengthHeuristic to get the median read length from a BAM...
read_slimmReads SLIMM output to a data table.
read_slimm_coverageReads SLIMM coverage to a data table.
remove_referenceRemoves sequence that map to a given reference.
replication_ratesEstimate replication rates by the iRep method.
selectVery simple select for mbtools artifacts. Just gets a...
silva_build_taxonomyBuild the lineages for the entire SILVA database.
slimmQuantifies abundances and coverage using SLIMM.
slimm_filesThe SLIMM taxonomy databases
sra_submissionPrepare submission files for the NCBI sequence read archive...
standardizeStandardize all continuous columns of a data frame.
taxa_countCounts the reads for a specific taxonomy level.
taxa_metricsCalculates what percentage of taxa was found in a reference...
taxa_quantsCompares taxa quantification from a measurement to a...
typesApplies the specified types to a data frame-like object.
with_classificationQuantify classification rates for each taxonomic rank.
Gibbons-Lab/mbtools documentation built on July 15, 2019, 5:28 p.m.