MicrobiotaProcess
an R package for analysis, visualization and biomarker discovery of microbiome

Package index
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Vignettes
Functions
276
Source code
44
Man pages
51
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MicrobiotaProcess: an R package for analysis, visualization and biomarker discovery of microbiome
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API

API for MicrobiotaProcess
an R package for analysis, visualization and biomarker discovery of microbiome

Global functions
DNAbin2DNASet Source code
LDAeffectsize Source code
addtaxlevel Source code
alphasample-class Man page
as.data.frame.alphasample Man page Source code Source code
as.data.frame.diffAnalysisClass Man page Source code Source code
as.treedata Man page
as.treedata.taxonomyTable Man page Source code
build_tree Man page
build_tree,DNAStringSet Man page
build_tree,DNAStringSet-method Man page
build_tree,DNAbin Man page
build_tree,DNAbin-method Man page
build_tree,character Man page
build_tree,character-method Man page
cal_ci Source code
checkotu Source code
checksample Source code
clustplotClass-class Man page
contribution Source code
convert_to_treedata Man page Source code
data-hmp_aerobiosis_small Man page
data-kostic2012crc Man page
data-test_otu_data Man page
diffAnalysisClass-class Man page
diff_analysis Man page Source code
diff_analysis.data.frame Man page Source code
diff_analysis.phyloseq Man page Source code
diffclass Source code
diffsubclass Source code
drop_taxa Man page
drop_taxa,data.frame Man page
drop_taxa,data.frame-method Man page
drop_taxa,phyloseq Man page
drop_taxa,phyloseq-method Man page
duplicatedtaxcheck Source code
extract_args Source code
fillNAtax Source code
filltaxname Source code
generalizedFC Man page Source code
generalizedFC.default Man page Source code
generalizedFC.formula Man page Source code
geom_ord_ellipse Source code
get_alltaxadf Man page
get_alltaxadf,data.frame Man page
get_alltaxadf,data.frame-method Man page
get_alltaxadf,phyloseq Man page
get_alltaxadf,phyloseq-method Man page
get_alltaxdf Source code
get_alphaindex Man page
get_alphaindex,data.frame Man page
get_alphaindex,data.frame-method Man page
get_alphaindex,integer Man page
get_alphaindex,integer-method Man page
get_alphaindex,matrix Man page
get_alphaindex,matrix-method Man page
get_alphaindex,numeric Man page
get_alphaindex,numeric-method Man page
get_alphaindex,phyloseq Man page
get_alphaindex,phyloseq-method Man page
get_annotlabel Source code
get_anova Source code
get_cladedf Source code
get_cladelabelposition Source code
get_class2sub Source code
get_classlevels Source code
get_clust Man page Source code
get_clust.data.frame Man page Source code
get_clust.dist Man page Source code
get_clust.phyloseq Man page Source code
get_compareclass Source code
get_comparelist Source code
get_compareres Source code
get_comparesubclass Source code
get_consistentfeatures Source code
get_coord Man page Source code
get_coord.pcoa Man page Source code
get_coord.prcomp Man page Source code
get_count Man page Source code
get_dist Man page Source code
get_dist.data.frame Man page Source code
get_dist.phyloseq Man page Source code
get_ellipsemap Source code
get_extend Source code
get_factormap Source code
get_gfc_wilc Source code
get_labeldf Source code
get_mean_median Man page Source code
get_node Source code
get_otudata Source code
get_pca Man page Source code
get_pca.data.frame Man page Source code
get_pca.phyloseq Man page Source code
get_pcoa Man page Source code
get_pcoa.data.frame Man page Source code
get_pcoa.dist Man page Source code
get_pcoa.phyloseq Man page Source code
get_pvalue Man page Source code
get_pvalue.QuadTypeIndependenceTest Man page Source code
get_pvalue.ScalarIndependenceTest Man page Source code
get_pvalue.glm Man page Source code
get_pvalue.htest Man page Source code
get_pvalue.lm Man page Source code
get_pvalue.lme Man page Source code
get_pvalue.negbin Man page Source code
get_rarecurve Man page
get_rarecurve,data.frame Man page
get_rarecurve,data.frame-method Man page
get_rarecurve,phyloseq Man page
get_rarecurve,phyloseq-method Man page
get_ratio Man page Source code
get_sample Source code
get_sampledflist Man page Source code
get_second_true_var Source code
get_secondvarlist Source code
get_taxadf Man page
get_taxadf,data.frame Man page
get_taxadf,data.frame-method Man page
get_taxadf,phyloseq Man page
get_taxadf,phyloseq-method Man page
get_upset Man page
get_upset,data.frame Man page
get_upset,data.frame-method Man page
get_upset,phyloseq Man page
get_upset,phyloseq-method Man page
get_varct Man page Source code
get_varct.pcasample Man page Source code
get_varct.pcoa Man page Source code
get_varct.prcomp Man page Source code
get_varlist Source code
get_vennlist Man page
get_vennlist,data.frame-method Man page
get_vennlist,data.framet Man page
get_vennlist,phyloseq Man page
get_vennlist,phyloseq-method Man page
ggbartax Man page Source code
ggbartax.data.frame Man page Source code
ggbartax.phyloseq Man page Source code
ggbartaxa Man page
ggbox Man page
ggbox,alphasample Man page
ggbox,alphasample-method Man page
ggbox,data.frame Man page
ggbox,data.frame-method Man page
ggclust Man page Source code
ggclust.clustplotClass Man page Source code
ggdiffbartaxa Man page
ggdiffbox Man page
ggdiffbox,diffAnalysisClass Man page
ggdiffbox,diffAnalysisClass-method Man page
ggdiffclade Man page Source code
ggdiffclade.data.frame Man page Source code
ggdiffclade.diffAnalysisClass Man page Source code
ggdifftaxbar Man page Source code
ggdifftaxbar,diffAnalysisClass Man page
ggdifftaxbar,diffAnalysisClass-method Man page
ggdifftaxbar.featureMeanMedian Man page Source code
ggeffectsize Man page Source code
ggeffectsize.data.frame Man page Source code
ggeffectsize.diffAnalysisClass Man page
ggordpoint Man page Source code
ggordpoint.default Man page Source code
ggordpoint.pcasample Man page Source code
ggrarecurve Man page Source code
ggrarecurve.data.frame Man page Source code
ggrarecurve.phyloseq Man page Source code
ggrarecurve.rarecurve Man page Source code
guess_rownames Source code
guides_diffclade Source code
hmp_aerobiosis_small Man page
import_dada2 Man page Source code
import_qiime2 Man page Source code
keep_know_taxa Source code
kostic2012crc Man page
mappingtaxda Source code
multi_compare Man page Source code
newtaxname Source code
ordplotClass-class Man page
pcasample-class Man page
pcoa-class Man page
plotdiffbox Source code
prcomp-class Man page
read.featuretab Source code
read.taxa Source code
read_qza Man page Source code
reexports Man page
remove_constant Source code
repduplicatedtaxcheck Source code
rfimportance Source code
samplealpha Source code
seedind Source code
set_factormap Source code
set_newlevels Source code
setfactorlevels Source code
show,diffAnalysisClass-method Man page
split_data Man page Source code
split_str_to_list Man page Source code
stat_rare Source code
test_otu_data Man page
theme_diffclade Source code
theme_taxbar Man page Source code
tidyEffectSize Source code
transformdf Source code
treeskeleton Source code
varcorf Source code
MicrobiotaProcess documentation built on April 18, 2021, 6 p.m.

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