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

.Rbuildignore
.gitignore
CONDUCT.md
DESCRIPTION
Makefile
NAMESPACE
NEWS.md R/AllClass.R R/alldata.R R/diff-analysis-utilities.R R/diff-ml-utilities.R R/method-MPSE-utilities.R R/method-accessor.R R/method-as-MPSE.R R/method-as-phyloseq.R R/method-as.data.frame.R R/method-as.treedata.R R/method-binary_offspring.R R/method-diff-analysis.R R/method-download-seq.R R/method-dplyr.R R/method-dr-tibble.R R/method-generalizedFC.R R/method-get-count-ratio.R R/method-io-utilities.R R/method-io.R R/method-mean-median.R R/method-mp_adonis_anosim.R R/method-mp_aggregate.R R/method-mp_aggregate_clade.R R/method-mp_cal_abundance.R R/method-mp_cal_alpha.R R/method-mp_cal_clust.R R/method-mp_cal_dist.R R/method-mp_cal_pca.R R/method-mp_cal_pcoa.R R/method-mp_cal_pd_metric.R R/method-mp_cal_rarecurve.R R/method-mp_cal_upset.R R/method-mp_cal_venn.R R/method-mp_decostand.R R/method-mp_diff_analysis.R R/method-mp_diff_clade.R R/method-mp_envfit.R R/method-mp_filter_taxa.R R/method-mp_fortify.R R/method-mp_mantel.R R/method-mp_rda_cca.R R/method-mp_rrarefy.R R/method-mp_stat_taxa.R R/method-related_phylo_metric.R R/method-show.R R/method-tibble.R R/method-tidyr.R R/plot-ggbartaxa.R R/plot-ggbox.R R/plot-ggclust.R R/plot-ggdiffbartaxa.R R/plot-ggdiffbox.R R/plot-ggdiffclade-utilities.R R/plot-ggdiffclade.R R/plot-ggeffectsize.R R/plot-ggordpoint-utilities.R R/plot-ggordpoint.R R/plot-ggrarecurve.R R/plot-methods.R R/reexports.R R/taxa_utilities.R R/tidy_utilities.R R/utilities.R R/zzz.R README.Rmd README.md
data/datalist
data/hmp_aerobiosis_small.rda
data/kostic2012crc.rda
data/mouse.time.mpse.rda
data/test_otu_data.rda
inst/extdata/MetaPhlAn/metaphlan_test.txt
inst/extdata/MetaPhlAn/sample_test.txt
inst/extdata/metadata_qza.txt
inst/extdata/mouse.time.dada2.txt
inst/extdata/mouse_feature_matrix.txt
inst/extdata/mouse_sample_info.txt
inst/extdata/mouse_taxda.txt
inst/extdata/otu_tax_table.txt
inst/extdata/sample_info.txt
inst/extdata/seqtab.nochim.rds
inst/extdata/table.qza
inst/extdata/taxa.qza
inst/extdata/taxa_tab.rds
inst/figures/mp-design.png
inst/figures/mpse.png
man/ImportDada2.Rd man/ImportQiime2.Rd man/MPSE-accessors.Rd man/MPSE-class.Rd man/MPSE.Rd man/alphasample-class.Rd man/as.MPSE.Rd man/as.phyloseq.Rd man/as.treedata.Rd man/build_tree.Rd man/convert_to_treedata.Rd man/data-hmp_aerobiosis_small.Rd man/data-kostic2012crc.Rd man/data-test_otu_data.Rd man/diffAnalysisClass-class.Rd man/diff_analysis.Rd man/dr_extract.Rd man/drop_taxa.Rd man/extract_binary_offspring.Rd man/generalizedFC.Rd man/get_NRI_NTI-methods.Rd man/get_alltaxadf.Rd man/get_alphaindex.Rd man/get_clust.Rd man/get_coord.Rd man/get_count.Rd man/get_dist.Rd man/get_mean_median.Rd man/get_pca.Rd man/get_pcoa.Rd man/get_pvalue.Rd man/get_rarecurve.Rd man/get_sampledflist.Rd man/get_taxadf.Rd man/get_upset.Rd man/get_varct.Rd man/get_vennlist.Rd man/ggbartax.Rd man/ggbox.Rd man/ggclust.Rd man/ggdiffbox.Rd man/ggdiffclade.Rd man/ggdifftaxbar.Rd man/ggeffectsize.Rd man/ggordpoint.Rd man/ggrarecurve.Rd man/mouse.time.mpse.Rd man/mp_adonis-methods.Rd man/mp_aggregate-methods.Rd man/mp_aggregate_clade-methods.Rd man/mp_anosim-methods.Rd man/mp_balance_clade-methods.Rd man/mp_cal_abundance-methods.Rd man/mp_cal_alpha-methods.Rd man/mp_cal_cca-methods.Rd man/mp_cal_clust-methods.Rd man/mp_cal_dca-methods.Rd man/mp_cal_dist-methods.Rd man/mp_cal_divergence-methods.Rd man/mp_cal_nmds-methods.Rd man/mp_cal_pca-methods.Rd man/mp_cal_pcoa-methods.Rd man/mp_cal_pd_metric-methods.Rd man/mp_cal_rarecurve-methods.Rd man/mp_cal_rda-methods.Rd man/mp_cal_upset-methods.Rd man/mp_cal_venn-methods.Rd man/mp_decostand-methods.Rd man/mp_diff_analysis-methods.Rd man/mp_diff_clade-methods.Rd man/mp_dmn-methods.Rd man/mp_dmngroup-methods.Rd man/mp_envfit-methods.Rd man/mp_extract_abundance-methods.Rd man/mp_extract_assays-methods.Rd man/mp_extract_dist-methods.Rd man/mp_extract_feature-methods.Rd man/mp_extract_internal_attr-methods.Rd man/mp_extract_rarecurve-methods.Rd man/mp_extract_refseq-methods.Rd man/mp_extract_sample-methods.Rd man/mp_extract_taxonomy-methods.Rd man/mp_extract_tree-methods.Rd man/mp_filter_taxa-methods.Rd man/mp_fortify.Rd man/mp_import_biom.Rd man/mp_import_metaphlan.Rd man/mp_import_qiime.Rd man/mp_mantel-methods.Rd man/mp_mrpp-methods.Rd man/mp_plot_abundance-methods.Rd man/mp_plot_alpha-methods.Rd man/mp_plot_diff_boxplot-methods.Rd man/mp_plot_diff_cladogram.Rd man/mp_plot_diff_res-methods.Rd man/mp_plot_dist-methods.Rd man/mp_plot_ord-methods.Rd man/mp_plot_rarecurve-methods.Rd man/mp_plot_upset-methods.Rd man/mp_plot_venn-methods.Rd man/mp_rrarefy-methods.Rd man/mp_select_as_tip-methods.Rd man/mp_stat_taxa-methods.Rd man/multi_compare.Rd man/ordplotClass-class.Rd man/pcasample-class.Rd man/pcoa-class.Rd man/prcomp-class.Rd man/print.Rd man/read_qza.Rd man/reexports.Rd man/scale_fill_diff_cladogram.Rd man/set_diff_boxplot_color.Rd man/set_scale_theme.Rd man/show-methods.Rd man/split_data.Rd man/split_str_to_list.Rd man/theme_stamp.Rd man/theme_taxbar.Rd tests/testthat.R tests/testthat/test_balance_clade.R tests/testthat/test_convert.R tests/testthat/test_extractargs.R tests/testthat/test_gettax.R tests/testthat/test_getvennlist.R tests/testthat/test_multicompare.R vignettes/MicrobiotaProcess.Rmd
vignettes/mp-design.png
vignettes/mpse.png
vignettes/refer.bib
xiangpin/MicrobitaProcess documentation built on Oct. 4, 2022, 6:28 a.m.