NAMESPACE 2.48 KB
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# Generated by roxygen2: do not edit by hand

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export(ASVenn_fun)
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export(VENNFUN)
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export(aggregate_fun)
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export(aggregate_top_taxa)
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export(assign_taxo_fun)
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export(bars_fun)
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export(check_tax_fun)
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export(core_soft_fun)
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export(csv2phyloseq_fun)
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export(dada2_fun)
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export(decontam_fun)
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export(deseq2_fun)
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export(diversity_alpha_fun)
export(diversity_beta_fun)
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export(diversity_beta_light)
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export(export_to_stamp_fun)
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export(fill_tax_fun)
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export(generate_phyloseq_fun)
export(generate_tree_fun)
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export(heatmap_fun)
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export(idTaxa_assign)
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export(idtaxa_assign_fasta_fun)
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export(idtaxa_traindb)
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export(list_venn_fun)
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export(metacoder_fun)
export(metagenomeseq_fun)
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export(phy2cyto_fun)
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export(phy2tsv_fun)
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export(plsda_fun)
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export(prune_db_fun)
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export(rarefaction)
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export(split_table_fun)
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export(subset_fastx)
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export(taxid_fun)
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export(update_metadata_fun)
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import(Biostrings)
import(DECIPHER)
import(ShortRead)
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import(VennDiagram)
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import(dada2)
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import(decontam)
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import(digest)
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import(doParallel)
import(foreach)
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import(futile.logger)
import(ggplot2)
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import(metagenomeSeq)
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import(mixOmics)
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import(pairwiseAdonis)
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import(phyloseq)
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import(plotly)
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import(psadd)
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import(reshape2)
import(scales)
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import(vegan)
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importFrom(Biobase,AnnotatedDataFrame)
importFrom(Biobase,fData)
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importFrom(BiocGenerics,estimateSizeFactors)
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importFrom(Biostrings,DNAStringSet)
importFrom(DECIPHER,AlignSeqs)
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importFrom(DESeq2,DESeq)
importFrom(DESeq2,results)
importFrom(DESeq2,resultsNames)
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importFrom(dplyr,across)
importFrom(dplyr,group_by)
importFrom(dplyr,group_map)
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importFrom(ggpubr,ggtexttable)
importFrom(ggpubr,text_grob)
importFrom(ggpubr,ttheme)
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importFrom(glue,glue)
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importFrom(grid,grid.draw)
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importFrom(gridExtra,grid.arrange)
importFrom(gridExtra,marrangeGrob)
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importFrom(gtools,mixedsort)
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importFrom(htmlwidgets,saveWidget)
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importFrom(metacoder,calc_n_samples)
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importFrom(metacoder,calc_obs_props)
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importFrom(metacoder,calc_taxon_abund)
importFrom(metacoder,compare_groups)
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importFrom(metacoder,diverging_palette)
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importFrom(metacoder,filter_obs)
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importFrom(metacoder,heat_tree)
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importFrom(metacoder,parse_phyloseq)
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importFrom(metacoder,taxon_names)
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importFrom(metacoder,zero_low_counts)
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importFrom(microbiome,aggregate_taxa)
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importFrom(microbiome,core_members)
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importFrom(microbiome,top_taxa)
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importFrom(microbiome,transform)
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importFrom(nlme,lme)
importFrom(phangorn,NJ)
importFrom(phangorn,dist.ml)
importFrom(phangorn,phyDat)
importFrom(phangorn,pml)
importFrom(plotly,ggplotly)
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importFrom(ranacapa,ggrare)
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importFrom(reshape2,melt)
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importFrom(venn,venn)