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| # Generated by roxygen2: do not edit by hand | ||
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| export(betadiv) | ||
| export(betatest) | ||
| export(biomarker) | ||
| export(buildTree) | ||
| export(difftest) | ||
| export(distcolor) | ||
| export(do_aov) | ||
| export(do_ttest) | ||
| export(do_wilcox) | ||
| export(ldamarker) | ||
| export(lightcolor) | ||
| export(normalize) | ||
| export(otu_table) | ||
| export(phy_tree) | ||
| export(plotLDA) | ||
| export(plotalpha) | ||
| export(plotbar) | ||
| export(plotbeta) | ||
| export(plotdiff) | ||
| export(plotmarker) | ||
| export(plotquality) | ||
| export(preRef) | ||
| export(prefilter) | ||
| export(processSeq) | ||
| export(richness) | ||
| export(sample_data) | ||
| export(subset_samples) | ||
| export(subset_taxa) | ||
| export(tax_table) | ||
| importFrom(Biostrings,DNAStringSet) | ||
| importFrom(DECIPHER,AlignSeqs) | ||
| importFrom(DESeq2,DESeq) | ||
| importFrom(DESeq2,DESeqDataSetFromMatrix) | ||
| importFrom(DESeq2,counts) | ||
| importFrom(DESeq2,estimateDispersions) | ||
| importFrom(DESeq2,estimateSizeFactors) | ||
| importFrom(DESeq2,results) | ||
| importFrom(DESeq2,varianceStabilizingTransformation) | ||
| importFrom(MASS,lda) | ||
| importFrom(S4Vectors,DataFrame) | ||
| importFrom(SummarizedExperiment,assay) | ||
| export(.setcolnames) | ||
| export(convertplot) | ||
| export(indocx) | ||
| export(infigure) | ||
| export(inoffice) | ||
| export(inpptx) | ||
| export(todocx) | ||
| export(toffice) | ||
| export(tofigure) | ||
| export(tohtml) | ||
| export(topptx) | ||
| export(totable) | ||
| export(toxlsx) | ||
| importFrom(R.devices,devEval) | ||
| importFrom(broom,tidy) | ||
| importFrom(dada2,addSpecies) | ||
| importFrom(dada2,assignTaxonomy) | ||
| importFrom(dada2,dada) | ||
| importFrom(dada2,derepFastq) | ||
| importFrom(dada2,filterAndTrim) | ||
| importFrom(dada2,getSequences) | ||
| importFrom(dada2,getUniques) | ||
| importFrom(dada2,learnErrors) | ||
| importFrom(dada2,makeSequenceTable) | ||
| importFrom(dada2,mergePairs) | ||
| importFrom(dada2,plotQualityProfile) | ||
| importFrom(dada2,removeBimeraDenovo) | ||
| importFrom(dplyr,bind_rows) | ||
| importFrom(dplyr,do) | ||
| importFrom(dplyr,filter) | ||
| importFrom(dplyr,group_by) | ||
| importFrom(dplyr,group_by_at) | ||
| importFrom(dplyr,left_join) | ||
| importFrom(dplyr,mutate) | ||
| importFrom(dplyr,one_of) | ||
| importFrom(dplyr,pull) | ||
| importFrom(dplyr,select) | ||
| importFrom(dplyr,summarise) | ||
| importFrom(dplyr,summarize) | ||
| importFrom(dplyr,ungroup) | ||
| importFrom(dplyr,vars) | ||
| importFrom(edgeR,calcNormFactors) | ||
| importFrom(devEMF,emf) | ||
| importFrom(dplyr,filter_) | ||
| importFrom(dplyr,select_) | ||
| importFrom(flextable,align) | ||
| importFrom(flextable,autofit) | ||
| importFrom(flextable,body_add_flextable) | ||
| importFrom(flextable,bold) | ||
| importFrom(flextable,empty_blanks) | ||
| importFrom(flextable,flextable) | ||
| importFrom(flextable,font) | ||
| importFrom(flextable,hline) | ||
| importFrom(flextable,theme_booktabs) | ||
| importFrom(ggplot2,aes) | ||
| importFrom(ggplot2,aes_string) | ||
| importFrom(ggplot2,coord_flip) | ||
| importFrom(ggplot2,element_blank) | ||
| importFrom(ggplot2,element_text) | ||
| importFrom(ggplot2,geom_bar) | ||
| importFrom(ggplot2,geom_point) | ||
| importFrom(ggplot2,geom_text) | ||
| importFrom(ggplot2,ggplot) | ||
| importFrom(ggplot2,scale_color_manual) | ||
| importFrom(ggplot2,last_plot) | ||
| importFrom(ggplot2,scale_fill_manual) | ||
| importFrom(ggplot2,scale_y_continuous) | ||
| importFrom(ggplot2,stat_ellipse) | ||
| importFrom(ggplot2,theme) | ||
| importFrom(ggplot2,theme_light) | ||
| importFrom(ggplot2,xlab) | ||
| importFrom(ggplot2,ylab) | ||
| importFrom(ggpubr,facet) | ||
| importFrom(ggpubr,ggboxplot) | ||
| importFrom(ggpubr,ggdotchart) | ||
| importFrom(ggpubr,ggdotplot) | ||
| importFrom(ggpubr,ggviolin) | ||
| importFrom(ggpubr,stat_pvalue_manual) | ||
| importFrom(ggplotify,as.ggplot) | ||
| importFrom(ggplotify,as.grob) | ||
| importFrom(grDevices,col2rgb) | ||
| importFrom(grDevices,dev.cur) | ||
| importFrom(grDevices,dev.off) | ||
| importFrom(grDevices,dev.size) | ||
| importFrom(grDevices,hcl) | ||
| importFrom(grDevices,recordPlot) | ||
| importFrom(grDevices,rgb) | ||
| importFrom(graphics,plot) | ||
| importFrom(htmlwidgets,saveWidget) | ||
| importFrom(magick,image_ggplot) | ||
| importFrom(magick,image_raster) | ||
| importFrom(magick,image_read) | ||
| importFrom(magick,image_read_pdf) | ||
| importFrom(magick,image_read_svg) | ||
| importFrom(magick,image_write) | ||
| importFrom(magrittr,"%>%") | ||
| importFrom(phangorn,NJ) | ||
| importFrom(phangorn,dist.ml) | ||
| importFrom(phangorn,optim.pml) | ||
| importFrom(phangorn,phyDat) | ||
| importFrom(phangorn,pml) | ||
| importFrom(phangorn,pml.control) | ||
| importFrom(phyloseq,'tax_table<-') | ||
| importFrom(phyloseq,`otu_table<-`) | ||
| importFrom(phyloseq,distance) | ||
| importFrom(phyloseq,estimate_richness) | ||
| importFrom(phyloseq,get_taxa_unique) | ||
| importFrom(phyloseq,nsamples) | ||
| importFrom(phyloseq,ordinate) | ||
| importFrom(phyloseq,otu_table) | ||
| importFrom(phyloseq,phyloseq) | ||
| importFrom(phyloseq,prune_taxa) | ||
| importFrom(phyloseq,psmelt) | ||
| importFrom(phyloseq,sample_data) | ||
| importFrom(phyloseq,subset_taxa) | ||
| importFrom(phyloseq,t) | ||
| importFrom(phyloseq,tax_table) | ||
| importFrom(phyloseq,taxa_are_rows) | ||
| importFrom(phyloseq,taxa_sums) | ||
| importFrom(phyloseq,transform_sample_counts) | ||
| importFrom(plyr,ddply) | ||
| importFrom(randomForest,importance) | ||
| importFrom(randomForest,randomForest) | ||
| importFrom(rlang,`!!`) | ||
| importFrom(rstatix,anova_test) | ||
| importFrom(rstatix,t_test) | ||
| importFrom(rstatix,wilcox_test) | ||
| importFrom(stats,as.formula) | ||
| importFrom(stats,kruskal.test) | ||
| importFrom(stats,p.adjust) | ||
| importFrom(stats,reorder) | ||
| importFrom(stats,update) | ||
| importFrom(tidyr,gather) | ||
| importFrom(tidyr,spread) | ||
| importFrom(utils,download.file) | ||
| importFrom(utils,head) | ||
| importFrom(utils,read.delim) | ||
| importFrom(utils,write.table) | ||
| importFrom(vegan,adonis) | ||
| importFrom(vegan,diversity) | ||
| importFrom(vegan,rarefy) | ||
| importFrom(vegan,specnumber) | ||
| importFrom(officer,add_slide) | ||
| importFrom(officer,body_add_img) | ||
| importFrom(officer,body_add_par) | ||
| importFrom(officer,docx_summary) | ||
| importFrom(officer,fp_border) | ||
| importFrom(officer,ph_location) | ||
| importFrom(officer,ph_location_type) | ||
| importFrom(officer,ph_with) | ||
| importFrom(officer,pptx_summary) | ||
| importFrom(officer,read_docx) | ||
| importFrom(officer,read_pptx) | ||
| importFrom(officer,read_xlsx) | ||
| importFrom(officer,slide_size) | ||
| importFrom(plotly,as_widget) | ||
| importFrom(plotly,ggplotly) | ||
| importFrom(rvg,dml) | ||
| importFrom(rvg,xl_add_vg) | ||
| importFrom(stats,formula) | ||
| importFrom(utils,type.convert) |