xiangpin/MicrobiotaProcess
A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

Package index
Search the xiangpin/MicrobiotaProcess package
Vignettes
Functions
962
Source code
72
Man pages
120
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xiangpin/MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework
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API

API for xiangpin/MicrobiotaProcess
A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

Global functions
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.aggregate_clade Source code
.as.MPSE.TSE Source code
.as.MPSE.biom Source code
.as.MPSE.grouped_df_mpse Source code
.as.MPSE.phyloseq Source code
.as.MPSE.tbl_mpse Source code
.as_tibble.mp.internal Source code
.as_tibble_MPSE Source code
.balance_clade Source code
.balance_offspring_node Source code
.build_mpse Source code
.build_ps Source code
.build_up_and_down Source code
.check_tree_tiplab Source code
.combine_others Source code
.convert_balance_tip2ancestors Source code
.convert_tips2ancestors_sbp Source code
.dist_to_df Source code
.extract_nodes Source code
.generate_tip.len Source code
.internal_aggregate Source code
.internal_append Source code
.internal_apply_cal_rarecurve Source code
.internal_balance Source code
.internal_build_assay Source code
.internal_cal_adonis Source code
.internal_cal_aed Source code
.internal_cal_all_pd_metric Source code
.internal_cal_anosim_mrpp Source code
.internal_cal_clust Source code
.internal_cal_dca Source code
.internal_cal_dist Source code
.internal_cal_divergence Source code
.internal_cal_dmn Source code
.internal_cal_dmngroup Source code
.internal_cal_eaed Source code
.internal_cal_envfit Source code
.internal_cal_feature_abun Source code
.internal_cal_haed Source code
.internal_cal_iac Source code
.internal_cal_inode Source code
.internal_cal_nmds Source code
.internal_cal_nri Source code
.internal_cal_nti Source code
.internal_cal_pae Source code
.internal_cal_pca Source code
.internal_cal_pcoa Source code
.internal_cal_pd_metric Source code
.internal_cal_pd_metric_ Source code
.internal_cal_rda_cca1 Source code
.internal_cal_rda_cca2 Source code
.internal_cal_upset Source code
.internal_cal_venn Source code
.internal_check_mutate Source code
.internal_check_taxonomy Source code
.internal_decostand Source code
.internal_denom Source code
.internal_extract_abundance Source code
.internal_extract_binary Source code
.internal_extract_sample Source code
.internal_extract_taxonomy_ Source code
.internal_filter_taxa Source code
.internal_import_dada2 Source code
.internal_import_qiime Source code
.internal_import_qiime2 Source code
.internal_mntd Source code
.internal_mp_aggregate Source code
.internal_mp_cal_alpha Source code
.internal_mp_cal_rarecurve Source code
.internal_mp_cal_upset Source code
.internal_mp_cal_venn Source code
.internal_mp_diff_analysis Source code
.internal_mp_diff_clade Source code
.internal_mp_mantel Source code
.internal_mp_rrarefy Source code
.internal_mpd Source code
.internal_nest Source code
.internal_nest_tibble Source code
.internal_plot_abundance Source code
.internal_reroot Source code
.internal_stat_taxa Source code
.internal_tax_table Source code
.internal_taxonomy Source code
.internal_valid_rare Source code
.make_random_label Source code
.onAttach Source code
.return_wrap Source code
.valid.MPSE Source code
ImportDada2 Man page
ImportQiime2 Man page
LDAeffectsize Source code
MPSE Man page Source code
MPSE-accessors Man page
MPSE-class Man page
MP_citations Source code
[,MPSE,ANY,ANY,ANY-method Man page
`$.diffAnalysisClass` Source code
`[.diffAnalysisClass` Source code
`[.tbl_mpse` Source code
`[[.diffAnalysisClass` Source code
add_attr Source code
add_internal_attr Source code
add_total_attr Source code
addtaxlevel Source code
alphasample-class Man page
arrange Man page
arrange.MPSE Source code
arrange.grouped_df_mpse Source code
arrange.tbl_mpse Source code
as.MPSE Man page Source code
as.data.frame.MPSE Source code
as.data.frame.alphasample Source code
as.data.frame.diffAnalysisClass Source code
as.mpse Man page
as.phyloseq Man page Source code
as.phyloseq.MPSE Man page Source code
as.phyloseq.tbl_mpse Man page
as.tbl_mpse Source code
as.tbl_mpse.data.frame Source code
as.treedata Man page
as.treedata.taxonomyTable Man page Source code
as.treedata.treedata Source code
as_phyloseq Man page
as_tibble Man page
as_tibble.DFrame Source code
as_tibble.MPSE Source code
as_tibble.grouped_df_mpse Source code
as_tibble.phyloseq Source code
avoid_conflict_names 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_Unifrac_dist Source code
cal_ci Source code
cal_dist_hopach Source code
cal_treedist Source code Source code
check_second_fun Source code
check_single_nrow_in_nest Source code
check_symbols Source code
checkotu Source code
checksample Source code
colData Man page
colData<- Man page
colData<-,MPSE,DataFrame-method Man page
colData<-,MPSE,NULL-method Man page
compare_mean Source code
compare_mean.default Source code
compare_mean.formula Source code
compare_median Source code
compare_median.formula Source code
contribution Source code
convert_to_treedata Man page Source code
convert_to_treedata2 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
dim.diffAnalysisClass Source code
distinct Man page
distinct.MPSE Source code
distinct.grouped_df_mpse Source code
distinct.tbl_mpse Source code
dr_extract Man page Source code
drop_class 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 Man page
extract_args Source code
extract_binary_offspring Man page Source code
extract_binary_offspring.phylo Source code
extract_binary_offspring.treedata Source code
extract_first_vars Source code
fillNAtax Source code
filltaxname Source code
filter Man page
filter.MPSE Source code
filter.alphasample Source code
filter.diffAnalysisClass Source code
filter.grouped_df_mpse Source code
filter.tbl_mpse Source code
formatted_out Source code
fortify Man page
fortify.MPSE Source code
fortify.SummarizedExperiment Source code
generalizedFC Man page Source code
generalizedFC.default Man page Source code
generalizedFC.formula Man page Source code
geom_ord_ellipse Source code
geometric.mean Source code
get_NRI_NTI Man page
get_NRI_NTI,data.frame Man page
get_NRI_NTI,data.frame-method Man page
get_NRI_NTI,matrix Man page
get_NRI_NTI,matrix-method Man page
get_NRI_NTI,phyloseq Man page
get_NRI_NTI,phyloseq-method Man page
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_anova 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_factormap Source code
get_gfc_wilc 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.treedata 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
grepl.data.frame Source code
group_by Man page
group_by.MPSE Source code
group_by.tbl_mpse Source code
head.alphasample Source code
head.diffAnalysisClass Source code
hmp_aerobiosis_small Man page
import_dada2 Man page Source code
import_qiime2 Man page Source code
internal_filter Source code
internal_select Source code
keep_know_taxa Source code
keep_mpse_message Source code
kostic2012crc Man page
left_join Man page
left_join.MPSE Source code
mappingtaxda Source code
merge_total_res Source code
message_wrap Source code
modify_AsIs_list Source code
mouse.time.mpse Man page
mp_adonis Man page
mp_adonis,MPSE Man page
mp_adonis,MPSE-method Man page
mp_adonis,grouped_df_mpse Man page
mp_adonis,grouped_df_mpse-method Man page
mp_adonis,tbl_mpse Man page
mp_adonis,tbl_mpse-method Man page
mp_aggregate Man page
mp_aggregate,MPSE Man page
mp_aggregate,MPSE-method Man page
mp_aggregate_clade Man page
mp_aggregate_clade,MPSE Man page
mp_aggregate_clade,MPSE-method Man page
mp_aggregate_clade,grouped_df_mpse Man page
mp_aggregate_clade,grouped_df_mpse-method Man page
mp_aggregate_clade,tbl_mpse Man page
mp_aggregate_clade,tbl_mpse-method Man page
mp_anosim Man page
mp_anosim,MPSE Man page
mp_anosim,MPSE-method Man page
mp_anosim,grouped_df_mpse Man page
mp_anosim,grouped_df_mpse-method Man page
mp_anosim,tbl_mpse Man page
mp_anosim,tbl_mpse-method Man page
mp_balance_clade Man page
mp_balance_clade,MPSE Man page
mp_balance_clade,MPSE-method Man page
mp_balance_clade,grouped_df_mpse Man page
mp_balance_clade,grouped_df_mpse-method Man page
mp_balance_clade,tbl_mpse Man page
mp_balance_clade,tbl_mpse-method Man page
mp_cal_abundance Man page
mp_cal_abundance,MPSE Man page
mp_cal_abundance,MPSE-method Man page
mp_cal_abundance,grouped_df_mpse Man page
mp_cal_abundance,grouped_df_mpse-method Man page
mp_cal_abundance,tbl_mpse Man page
mp_cal_abundance,tbl_mpse-method Man page
mp_cal_alpha Man page
mp_cal_alpha,MPSE Man page
mp_cal_alpha,MPSE-method Man page
mp_cal_alpha,grouped_df_mpse Man page
mp_cal_alpha,grouped_df_mpse-method Man page
mp_cal_alpha,tbl_mpse Man page
mp_cal_alpha,tbl_mpse-method Man page
mp_cal_cca Man page
mp_cal_cca,MPSE Man page
mp_cal_cca,MPSE-method Man page
mp_cal_cca,grouped_df_mpse Man page
mp_cal_cca,grouped_df_mpse-method Man page
mp_cal_cca,tbl_mpse Man page
mp_cal_cca,tbl_mpse-method Man page
mp_cal_clust Man page
mp_cal_clust,MPSE Man page
mp_cal_clust,MPSE-method Man page
mp_cal_clust,grouped_df_mpse Man page
mp_cal_clust,grouped_df_mpse-method Man page
mp_cal_clust,tbl_mpse Man page
mp_cal_clust,tbl_mpse-method Man page
mp_cal_dca Man page
mp_cal_dca,MPSE Man page
mp_cal_dca,MPSE-method Man page
mp_cal_dca,grouped_df_mpse Man page
mp_cal_dca,grouped_df_mpse-method Man page
mp_cal_dca,tbl_mpse Man page
mp_cal_dca,tbl_mpse-method Man page
mp_cal_dist Man page
mp_cal_dist,MPSE Man page
mp_cal_dist,MPSE-method Man page
mp_cal_dist,grouped_df_mpse Man page
mp_cal_dist,grouped_df_mpse-method Man page
mp_cal_dist,tbl_mpse Man page
mp_cal_dist,tbl_mpse-method Man page
mp_cal_divergence Man page
mp_cal_divergence,MPSE Man page
mp_cal_divergence,MPSE-method Man page
mp_cal_divergence,grouped_df_mpse Man page
mp_cal_divergence,grouped_df_mpse-method Man page
mp_cal_divergence,tbl_mpse Man page
mp_cal_divergence,tbl_mpse-method Man page
mp_cal_nmds Man page
mp_cal_nmds,MPSE Man page
mp_cal_nmds,MPSE-method Man page
mp_cal_nmds,grouped_df_mpse Man page
mp_cal_nmds,grouped_df_mpse-method Man page
mp_cal_nmds,tbl_mpse Man page
mp_cal_nmds,tbl_mpse-method Man page
mp_cal_pca Man page
mp_cal_pca,MPSE Man page
mp_cal_pca,MPSE-method Man page
mp_cal_pca,grouped_df_mpse Man page
mp_cal_pca,grouped_df_mpse-method Man page
mp_cal_pca,tbl_mpse Man page
mp_cal_pca,tbl_mpse-method Man page
mp_cal_pcoa Man page
mp_cal_pcoa,MPSE Man page
mp_cal_pcoa,MPSE-method Man page
mp_cal_pcoa,grouped_df_mpse Man page
mp_cal_pcoa,grouped_df_mpse-method Man page
mp_cal_pcoa,tbl_mpse Man page
mp_cal_pcoa,tbl_mpse-method Man page
mp_cal_pd_metric Man page
mp_cal_pd_metric,MPSE Man page
mp_cal_pd_metric,MPSE-method Man page
mp_cal_pd_metric,grouped_df_mpse Man page
mp_cal_pd_metric,grouped_df_mpse-method Man page
mp_cal_pd_metric,tbl_mpse Man page
mp_cal_pd_metric,tbl_mpse-method Man page
mp_cal_rarecurve Man page
mp_cal_rarecurve,MPSE Man page
mp_cal_rarecurve,MPSE-method Man page
mp_cal_rarecurve,grouped_df_mpse Man page
mp_cal_rarecurve,grouped_df_mpse-method Man page
mp_cal_rarecurve,tbl_mpse Man page
mp_cal_rarecurve,tbl_mpse-method Man page
mp_cal_rda Man page
mp_cal_rda,MPSE Man page
mp_cal_rda,MPSE-method Man page
mp_cal_rda,grouped_df_mpse Man page
mp_cal_rda,grouped_df_mpse-method Man page
mp_cal_rda,tbl_mpse Man page
mp_cal_rda,tbl_mpse-method Man page
mp_cal_upset Man page
mp_cal_upset,MPSE Man page
mp_cal_upset,MPSE-method Man page
mp_cal_upset,grouped_df_mpse Man page
mp_cal_upset,grouped_df_mpse-method Man page
mp_cal_upset,tbl_mpse Man page
mp_cal_upset,tbl_mpse-method Man page
mp_cal_venn Man page
mp_cal_venn,MPSE Man page
mp_cal_venn,MPSE-method Man page
mp_cal_venn,grouped_df_mpse Man page
mp_cal_venn,grouped_df_mpse-method Man page
mp_cal_venn,tbl_mpse Man page
mp_cal_venn,tbl_mpse-method Man page
mp_decostand Man page
mp_decostand,MPSE Man page
mp_decostand,MPSE-method Man page
mp_decostand,data.frame Man page
mp_decostand,data.frame-method Man page
mp_decostand,grouped_df_mpse Man page
mp_decostand,grouped_df_mpse-method Man page
mp_decostand,tbl_mpse Man page
mp_decostand,tbl_mpse-method Man page
mp_diff_analysis Man page
mp_diff_analysis,MPSE Man page
mp_diff_analysis,MPSE-method Man page
mp_diff_analysis,grouped_df_mpse Man page
mp_diff_analysis,grouped_df_mpse-method Man page
mp_diff_analysis,tbl_mpse Man page
mp_diff_analysis,tbl_mpse-method Man page
mp_diff_clade Man page
mp_diff_clade,MPSE Man page
mp_diff_clade,MPSE-method Man page
mp_diff_clade,grouped_df_mpse Man page
mp_diff_clade,grouped_df_mpse-method Man page
mp_diff_clade,tbl_mpse Man page
mp_diff_clade,tbl_mpse-method Man page
mp_dmn Man page
mp_dmn,MPSE Man page
mp_dmn,MPSE-method Man page
mp_dmn,grouped_df_mpse Man page
mp_dmn,grouped_df_mpse-method Man page
mp_dmn,tbl_mpse Man page
mp_dmn,tbl_mpse-method Man page
mp_dmngroup Man page
mp_dmngroup,MPSE Man page
mp_dmngroup,MPSE-method Man page
mp_dmngroup,grouped_df_mpse Man page
mp_dmngroup,grouped_df_mpse-method Man page
mp_dmngroup,tbl_mpse Man page
mp_dmngroup,tbl_mpse-method Man page
mp_envfit Man page
mp_envfit,MPSE Man page
mp_envfit,MPSE-method Man page
mp_envfit,grouped_df_mpse Man page
mp_envfit,grouped_df_mpse-method Man page
mp_envfit,tbl_mpse Man page
mp_envfit,tbl_mpse-method Man page
mp_extract_abundance Man page
mp_extract_abundance,MPSE Man page
mp_extract_abundance,MPSE-method Man page
mp_extract_abundance,grouped_df_mpse Man page
mp_extract_abundance,grouped_df_mpse-method Man page
mp_extract_abundance,tbl_mpse Man page
mp_extract_abundance,tbl_mpse-method Man page
mp_extract_assays Man page
mp_extract_assays,MPSE Man page
mp_extract_assays,MPSE-method Man page
mp_extract_assays,grouped_df_mpse Man page
mp_extract_assays,grouped_df_mpse-method Man page
mp_extract_assays,tbl_mpse Man page
mp_extract_assays,tbl_mpse-method Man page
mp_extract_dist Man page
mp_extract_dist,MPSE Man page
mp_extract_dist,MPSE-method Man page
mp_extract_dist,grouped_df_mpse Man page
mp_extract_dist,grouped_df_mpse-method Man page
mp_extract_dist,tbl_mpse Man page
mp_extract_dist,tbl_mpse-method Man page
mp_extract_feature Man page
mp_extract_feature,MPSE Man page
mp_extract_feature,MPSE-method Man page
mp_extract_feature,grouped_df_mpse Man page
mp_extract_feature,grouped_df_mpse-method Man page
mp_extract_feature,tbl_mpse Man page
mp_extract_feature,tbl_mpse-method Man page
mp_extract_internal_attr Man page
mp_extract_internal_attr,MPSE Man page
mp_extract_internal_attr,MPSE-method Man page
mp_extract_internal_attr,grouped_df_mpse Man page
mp_extract_internal_attr,grouped_df_mpse-method Man page
mp_extract_internal_attr,tbl_mpse Man page
mp_extract_internal_attr,tbl_mpse-method Man page
mp_extract_otutree Man page Source code
mp_extract_rarecurve Man page
mp_extract_rarecurve,MPSE Man page
mp_extract_rarecurve,MPSE-method Man page
mp_extract_rarecurve,grouped_df_mpse Man page
mp_extract_rarecurve,grouped_df_mpse-method Man page
mp_extract_rarecurve,tbl_mpse Man page
mp_extract_rarecurve,tbl_mpse-method Man page
mp_extract_refseq Man page
mp_extract_refseq,MPSE Man page
mp_extract_refseq,MPSE-method Man page
mp_extract_refseq,grouped_df_mpse Man page
mp_extract_refseq,grouped_df_mpse-method Man page
mp_extract_refseq,tbl_mpse Man page
mp_extract_refseq,tbl_mpse-method Man page
mp_extract_sample Man page
mp_extract_sample,MPSE Man page
mp_extract_sample,MPSE-method Man page
mp_extract_sample,grouped_df_mpse Man page
mp_extract_sample,grouped_df_mpse-method Man page
mp_extract_sample,tbl_mpse Man page
mp_extract_sample,tbl_mpse-method Man page
mp_extract_taxatree Man page Source code
mp_extract_taxonomy Man page
mp_extract_taxonomy,MPSE Man page
mp_extract_taxonomy,MPSE-method Man page
mp_extract_taxonomy,grouped_df_mpse Man page
mp_extract_taxonomy,grouped_df_mpse-method Man page
mp_extract_taxonomy,tbl_mpse Man page
mp_extract_taxonomy,tbl_mpse-method Man page
mp_extract_tree Man page
mp_extract_tree,MPSE Man page
mp_extract_tree,MPSE-method Man page
mp_extract_tree,grouped_df_mpse Man page
mp_extract_tree,grouped_df_mpse-method Man page
mp_extract_tree,tbl_mpse Man page
mp_extract_tree,tbl_mpse-method Man page
mp_filter_taxa Man page
mp_filter_taxa,MPSE Man page
mp_filter_taxa,MPSE-method Man page
mp_filter_taxa,grouped_df_mpse Man page
mp_filter_taxa,grouped_df_mpse-method Man page
mp_filter_taxa,tbl_mpse Man page
mp_filter_taxa,tbl_mpse-method Man page
mp_fortify Man page Source code
mp_fortify.anosim Source code
mp_fortify.anova.cca Source code
mp_fortify.envfit Source code
mp_fortify.mantel Source code
mp_fortify.mantel.partial Source code
mp_fortify.mrpp Source code
mp_import_biom Man page Source code
mp_import_dada2 Man page Source code
mp_import_humann_regroup Man page
mp_import_metaphlan Man page Source code
mp_import_qiime Man page Source code
mp_import_qiime2 Man page Source code
mp_mantel Man page
mp_mantel,MPSE Man page
mp_mantel,MPSE-method Man page
mp_mantel,grouped_df_mpse Man page
mp_mantel,grouped_df_mpse-method Man page
mp_mantel,tbl_mpse Man page
mp_mantel,tbl_mpse-method Man page
mp_mrpp Man page
mp_mrpp,MPSE Man page
mp_mrpp,MPSE-method Man page
mp_mrpp,grouped_df_mpse Man page
mp_mrpp,grouped_df_mpse-method Man page
mp_mrpp,tbl_mpse Man page
mp_mrpp,tbl_mpse-method Man page
mp_plot_abundance Man page
mp_plot_abundance,MPSE Man page
mp_plot_abundance,MPSE-method Man page
mp_plot_abundance,grouped_df_mpse Man page
mp_plot_abundance,grouped_df_mpse-method Man page
mp_plot_abundance,tbl_mpse Man page
mp_plot_abundance,tbl_mpse-method Man page
mp_plot_alpha Man page
mp_plot_alpha,MPSE Man page
mp_plot_alpha,MPSE-method Man page
mp_plot_alpha,grouped_df_mpse Man page
mp_plot_alpha,grouped_df_mpse-method Man page
mp_plot_alpha,tbl_mpse Man page
mp_plot_alpha,tbl_mpse-method Man page
mp_plot_diff_boxplot Man page
mp_plot_diff_boxplot,MPSE Man page
mp_plot_diff_boxplot,MPSE-method Man page
mp_plot_diff_boxplot,grouped_df_mpse Man page
mp_plot_diff_boxplot,grouped_df_mpse-method Man page
mp_plot_diff_boxplot,tbl_mpse Man page
mp_plot_diff_boxplot,tbl_mpse-method Man page
mp_plot_diff_cladogram Man page
mp_plot_diff_manhattan Man page
mp_plot_diff_manhattan,MPSE Man page
mp_plot_diff_manhattan,MPSE-method Man page
mp_plot_diff_manhattan,grouped_df_mpse Man page
mp_plot_diff_manhattan,grouped_df_mpse-method Man page
mp_plot_diff_manhattan,tbl_mpse Man page
mp_plot_diff_manhattan,tbl_mpse-method Man page
mp_plot_diff_res Man page
mp_plot_diff_res,MPSE Man page
mp_plot_diff_res,MPSE-method Man page
mp_plot_diff_res,grouped_df_mpse Man page
mp_plot_diff_res,grouped_df_mpse-method Man page
mp_plot_diff_res,tbl_mpse Man page
mp_plot_diff_res,tbl_mpse-method Man page
mp_plot_dist Man page
mp_plot_dist,MPSE Man page
mp_plot_dist,MPSE-method Man page
mp_plot_dist,grouped_df_mpse Man page
mp_plot_dist,grouped_df_mpse-method Man page
mp_plot_dist,tbl_mpse Man page
mp_plot_dist,tbl_mpse-method Man page
mp_plot_ord Man page
mp_plot_ord,MPSE Man page
mp_plot_ord,MPSE-method Man page
mp_plot_ord,grouped_df_mpse Man page
mp_plot_ord,grouped_df_mpse-method Man page
mp_plot_ord,tbl_mpse Man page
mp_plot_ord,tbl_mpse-method Man page
mp_plot_rarecurve Man page
mp_plot_rarecurve,MPSE Man page
mp_plot_rarecurve,MPSE-method Man page
mp_plot_rarecurve,grouped_df_mpse-method Man page
mp_plot_rarecurve,grouped_tbl_mpse Man page
mp_plot_rarecurve,tbl_mpse Man page
mp_plot_rarecurve,tbl_mpse-method Man page
mp_plot_upset Man page
mp_plot_upset,MPSE Man page
mp_plot_upset,MPSE-method Man page
mp_plot_upset,grouped_df_mpse Man page
mp_plot_upset,grouped_df_mpse-method Man page
mp_plot_upset,tbl_mpse Man page
mp_plot_upset,tbl_mpse-method Man page
mp_plot_venn Man page
mp_plot_venn,MPSE Man page
mp_plot_venn,MPSE-method Man page
mp_plot_venn,grouped_df_mpse Man page
mp_plot_venn,grouped_df_mpse-method Man page
mp_plot_venn,tbl_mpse Man page
mp_plot_venn,tbl_mpse-method Man page
mp_rrarefy Man page
mp_rrarefy,MPSE Man page
mp_rrarefy,MPSE-method Man page
mp_rrarefy,grouped_df_mpse Man page
mp_rrarefy,grouped_df_mpse-method Man page
mp_rrarefy,tbl_mpse Man page
mp_rrarefy,tbl_mpse-method Man page
mp_select_as_tip Man page
mp_select_as_tip,MPSE Man page
mp_select_as_tip,MPSE-method Man page
mp_select_as_tip,grouped_df_mpse Man page
mp_select_as_tip,grouped_df_mpse-method Man page
mp_select_as_tip,tbl_mpse Man page
mp_select_as_tip,tbl_mpse-method Man page
mp_stat_taxa Man page
mp_stat_taxa,MPSE Man page
mp_stat_taxa,MPSE-method Man page
mp_stat_taxa,grouped_df_mpse Man page
mp_stat_taxa,grouped_df_mpse-method Man page
mp_stat_taxa,tbl_mpse Man page
mp_stat_taxa,tbl_mpse-method Man page
multi_compare Man page Source code
mutate Man page
mutate.MPSE Source code
mutate.grouped_df_mpse Source code
mutate.tbl_mpse Source code
nest Man page
nest.grouped_df_mpse Source code
nest.tbl_mpse Source code
nest_internal Source code
newtaxname Source code
ordplotClass-class Man page
otutree Man page
otutree,MPSE Man page
otutree,MPSE-method Man page
otutree,group_df_mpse Man page
otutree,tbl_mpse Man page
otutree,tbl_mpse-method Man page
otutree<- Man page
otutree<-,MPSE Man page
otutree<-,MPSE,NULL-method Man page
otutree<-,MPSE,phylo-method Man page
otutree<-,MPSE,treedata-method Man page
otutree<-,grouped_df_mpse Man page
otutree<-,grouped_df_mpse,NULL-method Man page
otutree<-,grouped_df_mpse,treedata-method Man page
otutree<-,tbl_mpse Man page
otutree<-,tbl_mpse,NULL-method Man page
otutree<-,tbl_mpse,treedata-method Man page
pcasample-class Man page
pcoa-class Man page
plotdiffbox Source code
prcomp-class Man page
print Man page
print.MPSE Man page Source code
print.alphasample Source code
print.grouped_df_mpse Man page
print.rarecurve Man page
print.tbl_mpse Man page
print1.MPSE Source code
print2.MPSE Source code
pull Man page
read_qiime_otu Source code
read_qza Man page
reexports Man page
refsequence Man page
refsequence,MPSE Man page
refsequence,MPSE-method Man page
refsequence<- Man page
refsequence<-,MPSE Man page
refsequence<-,MPSE,NULL-method Man page
refsequence<-,MPSE,XStringSet-method Man page
remove_MP_internal_res Source code
remove_constant Source code
remove_missing Man page
remove_unclassfied Source code
rename Man page
rename.MPSE Source code
rename.grouped_df_mpse Source code
rename.tbl_mpse Source code
repduplicatedtaxcheck Source code
rfimportance Source code
rowData Man page
rownames<-,MPSE Man page
rownames<-,MPSE-method Man page
samplealpha Source code
scale_fill_diff_cladogram Man page
seedind Source code
select Man page
select.MPSE Source code
select.alphasample Source code
select.diffAnalysisClass Source code
select.grouped_df_mpse Source code
select.tbl_mpse Source code
select_true_nm Source code
set_diff_boxplot_color Man page
set_factormap Source code
set_newlevels Source code
set_scale_theme Man page
setfactorlevels Source code
show,MPSE-method Man page
show,alphasample-method Man page
show,diffAnalysisClass-method Man page
slice Man page
split_data Man page Source code
split_str_to_list Man page Source code
stat_rare Source code
stop_wrap Source code
suppressmsg Source code
tail.diffAnalysisClass Source code
tax_table Man page
tax_table,MPSE Man page
tax_table,MPSE-method Man page
tax_table,grouped_df_mpse Man page
tax_table,grouped_df_mpse-method Man page
tax_table,tbl_mpse Man page
tax_table,tbl_mpse-method Man page
taxatree Man page
taxatree,MPSE Man page
taxatree,MPSE-method Man page
taxatree,grouped_df_mpse Man page
taxatree,grouped_df_mpse-method Man page
taxatree,tbl_mpse Man page
taxatree,tbl_mpse-method Man page
taxatree<- Man page
taxatree<-,MPSE Man page
taxatree<-,MPSE,NULL-method Man page
taxatree<-,MPSE,treedata-method Man page
taxatree<-,grouped_df_mpse Man page
taxatree<-,grouped_df_mpse,NULL-method Man page
taxatree<-,grouped_df_mpse,treedata-method Man page
taxatree<-,tbl_mpse Man page
taxatree<-,tbl_mpse,NULL-method Man page
taxatree<-,tbl_mpse,treedata-method Man page
taxonomy Man page
taxonomy,MPSE Man page
taxonomy,MPSE-method Man page
taxonomy,grouped_df_mpse Man page
taxonomy,grouped_df_mpse-method Man page
taxonomy,tbl_mpse Man page
taxonomy,tbl_mpse-method Man page
taxonomy<- Man page
taxonomy<-,MPSE Man page
taxonomy<-,MPSE,NULL-method Man page
taxonomy<-,MPSE,data.frame-method Man page
taxonomy<-,MPSE,matrix-method Man page
taxonomy<-,MPSE,taxonomyTable-method Man page
tbl_mpse_return_message Source code
td_filter Man page
td_unnest Man page
test_otu_data Man page
theme_diffclade Source code
theme_taxbar Man page Source code
tidydr Source code
tidydr.cca Source code
tidydr.decorana Source code
tidydr.metaMDS Source code
tidydr.pcoa Source code
tidydr.prcomp Source code
transformdf Source code
treeskeleton Source code
try_convert_taxa Source code
ungroup Man page
ungroup.grouped_df_mpse Source code
unnest Man page
unnest.tbl_mpse_nest Source code
valid_rare Source code
valid_rare.MPSE Source code
valid_rare.grouped_df_mpse Source code
valid_rare.tbl_mpse Source code
varcorf Source code
warning_wrap Source code
xiangpin/MicrobiotaProcess documentation built on Nov. 12, 2024, 2:05 p.m.

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