Man pages for ananata/fastq2otu
FASTQ2OTU: Automate microbiome analyses

assignSeqTaxonomy	Assign Taxonomy Uses DADA2's assignTaxonomy function to...
check_assign_tax	Check for valid inputs for fastAssignTaxa
check_fastPaired	Check for valid inputs for fastPaired
check_fastq2otu	Check for valid inputs for fastq2otu
check_fastSingle	Check for valid inputs for fastPaired
check_filt_params	Check for valid inputs for fastFilter
check_primer_trim	Check for valid inputs for fastPrimerTrim
check_seq_dump	Check for valid inputs for fastSeqDump
fastAssignTaxa-class	FASTASSIGNTAXA Custom Class
fastFilter-class	FASTFILTER Custom Class
fastPaired-class	Inherits methods and attributes from fastq2otu class Lists...
fastPlotQuality-class	FASTPLOTQUALITY Custom Class
fastPrimerTrim-class	FASTPRIMERTRIM Custom Class
fastq2otu-class	FASTQ2OTU Custom Super-Class
fastReport-class	FASTREPORT Custom Class
fastSeqDump-class	FASTSEQDUMP Custom Class
fastSingle-class	Inherits methods and attributes from fastq2otu class Lists...
filtTrim	Filter and trim single or paired-end data
getMeanQualityProfile	Get quality profile of a fastq file(s).
getSeqs	Download SRA data using fastq-dump Parses list of SRA...
mergeSamples	Merge OTU tables from different samples
plot_quality	Create a function the plots quality graphs on individual...
plotQuality	plotQuality
plotSeqOverlap	Plot the quality profile of paired-end data The figure...
readConfig	Read in a config file (preferred method)
removeChimeras	Remove Chimeric Sequences Enables the use of DADA2's...
runPipeline	Execute project workflow from FASTQ input to OTU output using...
saveSeqs	Save sequence frequency tables in RDS file
saveTaxonomyTables	Save OTU Tables
setFastAssignTaxa	Create a fastAssignTaxa object
setFastFilter	Create a fastFilter object
setFastPaired	Create a fastPaired object
setfastPlotQuality	Create a fastPlotQuality object
setFastPrimerTrim	Create a fastPrimerTrim object Users have the option of...
setFastReport	Create a fastReport object Users have the option of creating...
setFastSeqDump	Create a fastSeqDump object Users have the option of...
setFastSingle	Create a fastSingle object
trimAdapters	Remove primers from sequences