alphasample-class	alphasample-class
as.data.frame.alphasample	as.data.frame
as.data.frame.diffAnalysisClass	as.data.frame
build_tree	build_tree
build_tree,character	build_tree
build_tree,character-method	build_tree
build_tree,DNAbin	build_tree
build_tree,DNAbin-method	build_tree
build_tree,DNAStringSet	build_tree
build_tree,DNAStringSet-method	build_tree
clustplotClass-class	clustplotClass-class
convert_to_treedata	convert_to_treedata
data-hmp_aerobiosis_small	data-hmp_aerobiosis_small
data-kostic2012crc	data-kostic2012crc
data-test_otu_data	data-test_otu_data
diffAnalysisClass-class	diffAnalysisClass-class
diff_analysis	diff_analysis
diff_analysis.data.frame	diff_analysis
diff_analysis.phyloseq	diff_analysis
drop_taxa	drop_taxa
drop_taxa,data.frame	drop_taxa
drop_taxa,data.frame-method	drop_taxa
drop_taxa,phyloseq	drop_taxa
drop_taxa,phyloseq-method	drop_taxa
generalizedFC	generalizedFC
generalizedFC.default	generalizedFC
generalizedFC.formula	generalizedFC
geom_ord_ellipse	geom_ord_ellipse
get_alltaxadf	get_alltaxadf
get_alltaxadf,data.frame	get_alltaxadf
get_alltaxadf,data.frame-method	get_alltaxadf
get_alltaxadf,phyloseq	get_alltaxadf
get_alltaxadf,phyloseq-method	get_alltaxadf
get_alphaindex	get_alphaindex
get_alphaindex,data.frame	get_alphaindex
get_alphaindex,data.frame-method	get_alphaindex
get_alphaindex,integer	get_alphaindex
get_alphaindex,integer-method	get_alphaindex
get_alphaindex,matrix	get_alphaindex
get_alphaindex,matrix-method	get_alphaindex
get_alphaindex,numeric	get_alphaindex
get_alphaindex,numeric-method	get_alphaindex
get_alphaindex,phyloseq	get_alphaindex
get_alphaindex,phyloseq-method	get_alphaindex
get_clust	get_clust
get_clust.default	get_clust
get_clust.dist	get_clust
get_clust.phyloseq	get_clust
get_coord	get_coord
get_coord.pcoa	get_coord
get_coord.prcomp	get_coord
get_count	get_count
get_dist	get_dist
get_dist.default	get_dist
get_dist.phyloseq	get_dist
get_mean_median	get_mean_median
get_pca	get_pca
get_pca.default	get_pca
get_pca.phyloseq	get_pca
get_pcoa	get_pcoa
get_pcoa.default	get_pcoa
get_pcoa.dist	get_pcoa
get_pcoa.phyloseq	get_pcoa
get_pvalue	get_pvalue
get_pvalue.glm	get_pvalue
get_pvalue.htest	get_pvalue
get_pvalue.lm	get_pvalue
get_pvalue.lme	get_pvalue
get_pvalue.negbin	get_pvalue
get_pvalue.QuadTypeIndependenceTest	get_pvalue
get_pvalue.ScalarIndependenceTest	get_pvalue
get_ratio	get_count
get_sampledflist	get_sampledflist
get_taxadf	get_taxadf
get_taxadf,data.frame	get_taxadf
get_taxadf,data.frame-method	get_taxadf
get_taxadf,phyloseq	get_taxadf
get_taxadf,phyloseq-method	get_taxadf
get_upset	get_upset
get_upset,data.frame	get_upset
get_upset,data.frame-method	get_upset
get_upset,phyloseq	get_upset
get_upset,phyloseq-method	get_upset
get_varct	get_varct
get_varct.pcasample	get_varct
get_varct.pcoa	get_varct
get_varct.prcomp	get_varct
get_vennlist	get_vennlist
get_vennlist,data.frame-method	get_vennlist
get_vennlist,data.framet	get_vennlist
get_vennlist,phyloseq	get_vennlist
get_vennlist,phyloseq-method	get_vennlist
ggbartax	ggbartax
ggbartax.default	ggbartax
ggbartax.phyloseq	ggbartax
ggbox	ggbox
ggbox,alphasample	ggbox
ggbox,alphasample-method	ggbox
ggbox,data.frame	ggbox
ggbox,data.frame-method	ggbox
ggclust	ggclust
ggclust.clustplotClass	ggclust
ggdiffbox	ggdiffbox
ggdiffbox,diffAnalysisClass	ggdiffbox
ggdiffbox,diffAnalysisClass-method	ggdiffbox
ggdiffclade	ggdiffclade
ggdiffclade.data.frame	ggdiffclade
ggdiffclade.diffAnalysisClass	ggdiffclade
ggdifftaxbar	ggdifftaxbar
ggdifftaxbar,diffAnalysisClass	ggdifftaxbar
ggdifftaxbar,diffAnalysisClass-method	ggdifftaxbar
ggdifftaxbar.featureMeanMedian	ggdifftaxbar
ggeffectsize	ggeffectsize
ggeffectsize.data.frame	ggeffectsize
ggeffectsize.diffAnalysisClass	ggeffectsize
ggordpoint	ggordpoint
ggordpoint.default	ggordpoint
ggordpoint.pcasample	ggordpoint
ggrarecurve	ggrarecurve
ggrarecurve.default	ggrarecurve
ggrarecurve.phyloseq	ggrarecurve
hmp_aerobiosis_small	data-hmp_aerobiosis_small
import_dada2	import_dada2
import_qiime2	import_qiime2
kostic2012crc	data-kostic2012crc
mappingtaxda	mappingtaxda
multi_compare	multi_compare
ordplotClass-class	ordplotClass-class
pcasample-class	pcasample-class
pcoa-class	pcoa-class
prcomp-class	prcomp-class
read_qza	read_qza
show,diffAnalysisClass-method	show-methods
split_data	split_data
split_str_to_list	split_str_to_list
stat_rare	stat_rare
test_otu_data	data-test_otu_data
theme_taxbar	theme_taxbar
