NAMESPACE

# Generated by roxygen2: do not edit by hand

S3method(as.matrix,mbquant)
export(align_long_reads)
export(align_short_reads)
export(annotate_contigs)
export(as_phyloseq)
export(association)
export(combinatorial_association)
export(config_align_long)
export(config_align_short)
export(config_count)
export(config_demultiplex)
export(config_denoise)
export(config_preprocess)
export(config_reference)
export(config_sra)
export(count_transcripts)
export(demultiplex)
export(denoise)
export(discretize)
export(download_files)
export(filter_counts)
export(filter_reference)
export(find_read_files)
export(find_taxa)
export(merge_transcripts)
export(mock_plot)
export(mockrobiota)
export(mothur_to_dada)
export(normalize)
export(orlitsky)
export(plot_counts)
export(plot_entropy)
export(plot_lengths)
export(plot_qualities)
export(plot_taxa)
export(preprocess)
export(quality_control)
export(quality_profile)
export(read_bam)
export(read_blast)
export(read_slimm)
export(select)
export(silva_build_taxonomy)
export(slimm)
export(sra_files)
export(sra_submission)
export(standardize)
export(taxa_count)
export(taxa_metrics)
export(taxa_quants)
export(types)
export(with_classification)
import(ShortRead)
import(futile.logger)
import(ggplot2)
import(phyloseq)
importFrom(Biostrings,BStringSet)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,fasta.index)
importFrom(Biostrings,readAAStringSet)
importFrom(Biostrings,readDNAStringSet)
importFrom(Biostrings,reverseComplement)
importFrom(Biostrings,writeXStringSet)
importFrom(DESeq2,DESeq)
importFrom(DESeq2,DESeqDataSetFromMatrix)
importFrom(DESeq2,estimateSizeFactors)
importFrom(DESeq2,lfcShrink)
importFrom(DESeq2,results)
importFrom(DESeq2,resultsNames)
importFrom(DESeq2,sizeFactors)
importFrom(GenomicAlignments,readGAlignments)
importFrom(Hmisc,cut2)
importFrom(R.utils,gunzip)
importFrom(Rcpp,sourceCpp)
importFrom(Rsamtools,ScanBamParam)
importFrom(ShortRead,qa)
importFrom(dada2,addSpecies)
importFrom(dada2,assignTaxonomy)
importFrom(dada2,dada)
importFrom(dada2,filterAndTrim)
importFrom(dada2,getUniques)
importFrom(dada2,learnErrors)
importFrom(dada2,mergeSequenceTables)
importFrom(dada2,plotErrors)
importFrom(dada2,removeBimeraDenovo)
importFrom(data.table,":=")
importFrom(data.table,as.data.table)
importFrom(data.table,data.table)
importFrom(data.table,dcast)
importFrom(data.table,fread)
importFrom(data.table,melt)
importFrom(data.table,rbindlist)
importFrom(data.table,set)
importFrom(data.table,setDT)
importFrom(data.table,setkey)
importFrom(data.table,tstrsplit)
importFrom(data.table,uniqueN)
importFrom(digest,digest)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,scale_y_log10)
importFrom(ggplot2,xlab)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,topTable)
importFrom(limma,voom)
importFrom(pbapply,pbapply)
importFrom(pbapply,pblapply)
importFrom(pbapply,pbsapply)
importFrom(phyloseq,otu_table)
importFrom(phyloseq,sample_data)
importFrom(phyloseq,tax_table)
importFrom(scales,percent)
importFrom(stats,glm)
importFrom(stats,influence)
importFrom(stats,model.matrix)
importFrom(stats,p.adjust)
importFrom(stats,quantile)
importFrom(stats,reformulate)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stringr,str_match)
importFrom(stringr,str_match_all)
importFrom(stringr,str_replace)
importFrom(stringr,str_replace_all)
importFrom(stringr,str_split_fixed)
importFrom(stringr,str_trim)
importFrom(stringr,str_trunc)
importFrom(utils,combn)
importFrom(utils,download.file)
importFrom(utils,packageVersion)
importFrom(utils,read.table)
importFrom(utils,tar)
useDynLib(mbtools, .registration = TRUE)