├── .Rbuildignore ├── .gitignore ├── CONDUCT.md ├── DESCRIPTION ├── Makefile ├── NAMESPACE ├── NEWS.md ├── R ├── AllClass.R ├── alldata.R ├── diff-analysis-utilities.R ├── diff-ml-utilities.R ├── internals.R ├── method-MPSE-utilities.R ├── method-accessor.R ├── method-as-MPSE.R ├── method-as-phyloseq.R ├── method-as.data.frame.R ├── method-as.treedata.R ├── method-binary_offspring.R ├── method-diff-analysis.R ├── method-download-seq.R ├── method-dplyr.R ├── method-dr-tibble.R ├── method-generalizedFC.R ├── method-get-count-ratio.R ├── method-ggplot2.R ├── method-io-utilities.R ├── method-io.R ├── method-mean-median.R ├── method-mp_adonis_anosim.R ├── method-mp_aggregate.R ├── method-mp_aggregate_clade.R ├── method-mp_cal_abundance.R ├── method-mp_cal_alpha.R ├── method-mp_cal_clust.R ├── method-mp_cal_dist.R ├── method-mp_cal_pca.R ├── method-mp_cal_pcoa.R ├── method-mp_cal_pd_metric.R ├── method-mp_cal_rarecurve.R ├── method-mp_cal_upset.R ├── method-mp_cal_venn.R ├── method-mp_decostand.R ├── method-mp_diff_analysis.R ├── method-mp_diff_clade.R ├── method-mp_envfit.R ├── method-mp_filter_taxa.R ├── method-mp_fortify.R ├── method-mp_mantel.R ├── method-mp_rda_cca.R ├── method-mp_rrarefy.R ├── method-mp_stat_taxa.R ├── method-related_phylo_metric.R ├── method-show.R ├── method-tibble.R ├── method-tidyr.R ├── plot-ggbartaxa.R ├── plot-ggbox.R ├── plot-ggclust.R ├── plot-ggdiffbartaxa.R ├── plot-ggdiffbox.R ├── plot-ggdiffclade.R ├── plot-ggeffectsize.R ├── plot-ggordpoint-utilities.R ├── plot-ggordpoint.R ├── plot-ggrarecurve.R ├── plot-methods.R ├── reexports.R ├── taxa_utilities.R ├── tidy_utilities.R ├── utilities.R └── zzz.R ├── README.Rmd ├── README.md ├── data ├── datalist ├── hmp_aerobiosis_small.rda ├── kostic2012crc.rda ├── mouse.time.mpse.rda └── test_otu_data.rda ├── inst ├── CITATION ├── extdata │ ├── MetaPhlAn │ │ ├── metaphlan_test.txt │ │ └── sample_test.txt │ ├── metadata_qza.txt │ ├── mouse.time.dada2.txt │ ├── mouse_feature_matrix.txt │ ├── mouse_sample_info.txt │ ├── mouse_taxda.txt │ ├── otu_tax_table.txt │ ├── sample_info.txt │ ├── seqtab.nochim.rds │ ├── table.qza │ ├── taxa.qza │ └── taxa_tab.rds └── figures │ ├── mp-design.png │ └── mpse.png ├── man ├── ImportDada2.Rd ├── ImportQiime2.Rd ├── MPSE-accessors.Rd ├── MPSE-class.Rd ├── MPSE.Rd ├── alphasample-class.Rd ├── as.MPSE.Rd ├── as.phyloseq.Rd ├── as.treedata.Rd ├── build_tree.Rd ├── convert_to_treedata.Rd ├── data-hmp_aerobiosis_small.Rd ├── data-kostic2012crc.Rd ├── data-test_otu_data.Rd ├── diffAnalysisClass-class.Rd ├── diff_analysis.Rd ├── dr_extract.Rd ├── drop_taxa.Rd ├── extract_binary_offspring.Rd ├── generalizedFC.Rd ├── get_NRI_NTI-methods.Rd ├── get_alltaxadf.Rd ├── get_alphaindex.Rd ├── get_clust.Rd ├── get_coord.Rd ├── get_count.Rd ├── get_dist.Rd ├── get_mean_median.Rd ├── get_pca.Rd ├── get_pcoa.Rd ├── get_pvalue.Rd ├── get_rarecurve.Rd ├── get_sampledflist.Rd ├── get_taxadf.Rd ├── get_upset.Rd ├── get_varct.Rd ├── get_vennlist.Rd ├── ggbartax.Rd ├── ggbox.Rd ├── ggclust.Rd ├── ggdiffbox.Rd ├── ggdiffclade.Rd ├── ggdifftaxbar.Rd ├── ggeffectsize.Rd ├── ggordpoint.Rd ├── ggrarecurve.Rd ├── mouse.time.mpse.Rd ├── mp_adonis-methods.Rd ├── mp_aggregate-methods.Rd ├── mp_aggregate_clade-methods.Rd ├── mp_anosim-methods.Rd ├── mp_balance_clade-methods.Rd ├── mp_cal_abundance-methods.Rd ├── mp_cal_alpha-methods.Rd ├── mp_cal_cca-methods.Rd ├── mp_cal_clust-methods.Rd ├── mp_cal_dca-methods.Rd ├── mp_cal_dist-methods.Rd ├── mp_cal_divergence-methods.Rd ├── mp_cal_nmds-methods.Rd ├── mp_cal_pca-methods.Rd ├── mp_cal_pcoa-methods.Rd ├── mp_cal_pd_metric-methods.Rd ├── mp_cal_rarecurve-methods.Rd ├── mp_cal_rda-methods.Rd ├── mp_cal_upset-methods.Rd ├── mp_cal_venn-methods.Rd ├── mp_decostand-methods.Rd ├── mp_diff_analysis-methods.Rd ├── mp_diff_clade-methods.Rd ├── mp_dmn-methods.Rd ├── mp_dmngroup-methods.Rd ├── mp_envfit-methods.Rd ├── mp_extract_abundance-methods.Rd ├── mp_extract_assays-methods.Rd ├── mp_extract_dist-methods.Rd ├── mp_extract_feature-methods.Rd ├── mp_extract_internal_attr-methods.Rd ├── mp_extract_rarecurve-methods.Rd ├── mp_extract_refseq-methods.Rd ├── mp_extract_sample-methods.Rd ├── mp_extract_taxonomy-methods.Rd ├── mp_extract_tree-methods.Rd ├── mp_filter_taxa-methods.Rd ├── mp_fortify.Rd ├── mp_import_biom.Rd ├── mp_import_humann_regroup.Rd ├── mp_import_metaphlan.Rd ├── mp_import_qiime.Rd ├── mp_mantel-methods.Rd ├── mp_mrpp-methods.Rd ├── mp_plot_abundance-methods.Rd ├── mp_plot_alpha-methods.Rd ├── mp_plot_diff_boxplot-methods.Rd ├── mp_plot_diff_cladogram.Rd ├── mp_plot_diff_manhattan-methods.Rd ├── mp_plot_diff_res-methods.Rd ├── mp_plot_dist-methods.Rd ├── mp_plot_ord-methods.Rd ├── mp_plot_rarecurve-methods.Rd ├── mp_plot_upset-methods.Rd ├── mp_plot_venn-methods.Rd ├── mp_rrarefy-methods.Rd ├── mp_select_as_tip-methods.Rd ├── mp_stat_taxa-methods.Rd ├── multi_compare.Rd ├── ordplotClass-class.Rd ├── pcasample-class.Rd ├── pcoa-class.Rd ├── prcomp-class.Rd ├── print.Rd ├── read_qza.Rd ├── reexports.Rd ├── scale_fill_diff_cladogram.Rd ├── set_diff_boxplot_color.Rd ├── set_scale_theme.Rd ├── show-methods.Rd ├── split_data.Rd ├── split_str_to_list.Rd └── theme_taxbar.Rd ├── tests ├── testthat.R └── testthat │ ├── test_balance_clade.R │ ├── test_convert.R │ ├── test_extractargs.R │ ├── test_gettax.R │ ├── test_getvennlist.R │ └── test_multicompare.R └── vignettes ├── MicrobiotaProcess.Rmd ├── mp-design.png ├── mpse.png └── refer.bib /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/.gitignore -------------------------------------------------------------------------------- /CONDUCT.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/CONDUCT.md -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/Makefile -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/NAMESPACE -------------------------------------------------------------------------------- /NEWS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/NEWS.md -------------------------------------------------------------------------------- /R/AllClass.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/AllClass.R -------------------------------------------------------------------------------- /R/alldata.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/alldata.R -------------------------------------------------------------------------------- /R/diff-analysis-utilities.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/diff-analysis-utilities.R -------------------------------------------------------------------------------- /R/diff-ml-utilities.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/diff-ml-utilities.R -------------------------------------------------------------------------------- /R/internals.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/internals.R -------------------------------------------------------------------------------- /R/method-MPSE-utilities.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-MPSE-utilities.R -------------------------------------------------------------------------------- /R/method-accessor.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-accessor.R -------------------------------------------------------------------------------- /R/method-as-MPSE.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-as-MPSE.R -------------------------------------------------------------------------------- /R/method-as-phyloseq.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-as-phyloseq.R -------------------------------------------------------------------------------- /R/method-as.data.frame.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-as.data.frame.R -------------------------------------------------------------------------------- /R/method-as.treedata.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-as.treedata.R -------------------------------------------------------------------------------- /R/method-binary_offspring.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-binary_offspring.R -------------------------------------------------------------------------------- /R/method-diff-analysis.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-diff-analysis.R -------------------------------------------------------------------------------- /R/method-download-seq.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-download-seq.R -------------------------------------------------------------------------------- /R/method-dplyr.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-dplyr.R -------------------------------------------------------------------------------- /R/method-dr-tibble.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-dr-tibble.R -------------------------------------------------------------------------------- /R/method-generalizedFC.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-generalizedFC.R -------------------------------------------------------------------------------- /R/method-get-count-ratio.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-get-count-ratio.R -------------------------------------------------------------------------------- /R/method-ggplot2.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-ggplot2.R -------------------------------------------------------------------------------- /R/method-io-utilities.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-io-utilities.R -------------------------------------------------------------------------------- /R/method-io.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-io.R -------------------------------------------------------------------------------- /R/method-mean-median.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-mean-median.R -------------------------------------------------------------------------------- /R/method-mp_adonis_anosim.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-mp_adonis_anosim.R -------------------------------------------------------------------------------- /R/method-mp_aggregate.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-mp_aggregate.R -------------------------------------------------------------------------------- /R/method-mp_aggregate_clade.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-mp_aggregate_clade.R -------------------------------------------------------------------------------- /R/method-mp_cal_abundance.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-mp_cal_abundance.R -------------------------------------------------------------------------------- /R/method-mp_cal_alpha.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-mp_cal_alpha.R -------------------------------------------------------------------------------- /R/method-mp_cal_clust.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-mp_cal_clust.R -------------------------------------------------------------------------------- /R/method-mp_cal_dist.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-mp_cal_dist.R -------------------------------------------------------------------------------- /R/method-mp_cal_pca.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-mp_cal_pca.R -------------------------------------------------------------------------------- /R/method-mp_cal_pcoa.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-mp_cal_pcoa.R -------------------------------------------------------------------------------- /R/method-mp_cal_pd_metric.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-mp_cal_pd_metric.R -------------------------------------------------------------------------------- /R/method-mp_cal_rarecurve.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-mp_cal_rarecurve.R -------------------------------------------------------------------------------- /R/method-mp_cal_upset.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-mp_cal_upset.R -------------------------------------------------------------------------------- /R/method-mp_cal_venn.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-mp_cal_venn.R -------------------------------------------------------------------------------- /R/method-mp_decostand.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-mp_decostand.R -------------------------------------------------------------------------------- /R/method-mp_diff_analysis.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-mp_diff_analysis.R -------------------------------------------------------------------------------- /R/method-mp_diff_clade.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-mp_diff_clade.R -------------------------------------------------------------------------------- /R/method-mp_envfit.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-mp_envfit.R -------------------------------------------------------------------------------- /R/method-mp_filter_taxa.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-mp_filter_taxa.R -------------------------------------------------------------------------------- /R/method-mp_fortify.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-mp_fortify.R -------------------------------------------------------------------------------- /R/method-mp_mantel.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-mp_mantel.R -------------------------------------------------------------------------------- /R/method-mp_rda_cca.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-mp_rda_cca.R -------------------------------------------------------------------------------- /R/method-mp_rrarefy.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-mp_rrarefy.R -------------------------------------------------------------------------------- /R/method-mp_stat_taxa.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-mp_stat_taxa.R -------------------------------------------------------------------------------- /R/method-related_phylo_metric.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-related_phylo_metric.R -------------------------------------------------------------------------------- /R/method-show.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-show.R -------------------------------------------------------------------------------- /R/method-tibble.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-tibble.R -------------------------------------------------------------------------------- /R/method-tidyr.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/method-tidyr.R -------------------------------------------------------------------------------- /R/plot-ggbartaxa.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/plot-ggbartaxa.R -------------------------------------------------------------------------------- /R/plot-ggbox.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/plot-ggbox.R -------------------------------------------------------------------------------- /R/plot-ggclust.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/plot-ggclust.R -------------------------------------------------------------------------------- /R/plot-ggdiffbartaxa.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/plot-ggdiffbartaxa.R -------------------------------------------------------------------------------- /R/plot-ggdiffbox.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/plot-ggdiffbox.R -------------------------------------------------------------------------------- /R/plot-ggdiffclade.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/plot-ggdiffclade.R -------------------------------------------------------------------------------- /R/plot-ggeffectsize.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/plot-ggeffectsize.R -------------------------------------------------------------------------------- /R/plot-ggordpoint-utilities.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/plot-ggordpoint-utilities.R -------------------------------------------------------------------------------- /R/plot-ggordpoint.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/plot-ggordpoint.R -------------------------------------------------------------------------------- /R/plot-ggrarecurve.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/plot-ggrarecurve.R -------------------------------------------------------------------------------- /R/plot-methods.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/plot-methods.R -------------------------------------------------------------------------------- /R/reexports.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/reexports.R -------------------------------------------------------------------------------- /R/taxa_utilities.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/taxa_utilities.R -------------------------------------------------------------------------------- /R/tidy_utilities.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/tidy_utilities.R -------------------------------------------------------------------------------- /R/utilities.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/utilities.R -------------------------------------------------------------------------------- /R/zzz.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/R/zzz.R -------------------------------------------------------------------------------- /README.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/README.Rmd -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/README.md -------------------------------------------------------------------------------- /data/datalist: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/data/datalist -------------------------------------------------------------------------------- /data/hmp_aerobiosis_small.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/data/hmp_aerobiosis_small.rda -------------------------------------------------------------------------------- /data/kostic2012crc.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/data/kostic2012crc.rda -------------------------------------------------------------------------------- /data/mouse.time.mpse.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/data/mouse.time.mpse.rda -------------------------------------------------------------------------------- /data/test_otu_data.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/data/test_otu_data.rda -------------------------------------------------------------------------------- /inst/CITATION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/inst/CITATION -------------------------------------------------------------------------------- /inst/extdata/MetaPhlAn/metaphlan_test.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/inst/extdata/MetaPhlAn/metaphlan_test.txt -------------------------------------------------------------------------------- /inst/extdata/MetaPhlAn/sample_test.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/inst/extdata/MetaPhlAn/sample_test.txt -------------------------------------------------------------------------------- /inst/extdata/metadata_qza.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/inst/extdata/metadata_qza.txt -------------------------------------------------------------------------------- /inst/extdata/mouse.time.dada2.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/inst/extdata/mouse.time.dada2.txt -------------------------------------------------------------------------------- /inst/extdata/mouse_feature_matrix.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/inst/extdata/mouse_feature_matrix.txt -------------------------------------------------------------------------------- /inst/extdata/mouse_sample_info.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/inst/extdata/mouse_sample_info.txt -------------------------------------------------------------------------------- /inst/extdata/mouse_taxda.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/inst/extdata/mouse_taxda.txt -------------------------------------------------------------------------------- /inst/extdata/otu_tax_table.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/inst/extdata/otu_tax_table.txt -------------------------------------------------------------------------------- /inst/extdata/sample_info.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/inst/extdata/sample_info.txt -------------------------------------------------------------------------------- /inst/extdata/seqtab.nochim.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/inst/extdata/seqtab.nochim.rds -------------------------------------------------------------------------------- /inst/extdata/table.qza: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/inst/extdata/table.qza -------------------------------------------------------------------------------- /inst/extdata/taxa.qza: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/inst/extdata/taxa.qza -------------------------------------------------------------------------------- /inst/extdata/taxa_tab.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/inst/extdata/taxa_tab.rds -------------------------------------------------------------------------------- /inst/figures/mp-design.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/inst/figures/mp-design.png -------------------------------------------------------------------------------- /inst/figures/mpse.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/inst/figures/mpse.png -------------------------------------------------------------------------------- /man/ImportDada2.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/ImportDada2.Rd -------------------------------------------------------------------------------- /man/ImportQiime2.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/ImportQiime2.Rd -------------------------------------------------------------------------------- /man/MPSE-accessors.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/MPSE-accessors.Rd -------------------------------------------------------------------------------- /man/MPSE-class.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/MPSE-class.Rd -------------------------------------------------------------------------------- /man/MPSE.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/MPSE.Rd -------------------------------------------------------------------------------- /man/alphasample-class.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/alphasample-class.Rd -------------------------------------------------------------------------------- /man/as.MPSE.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/as.MPSE.Rd -------------------------------------------------------------------------------- /man/as.phyloseq.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/as.phyloseq.Rd -------------------------------------------------------------------------------- /man/as.treedata.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/as.treedata.Rd -------------------------------------------------------------------------------- /man/build_tree.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/build_tree.Rd -------------------------------------------------------------------------------- /man/convert_to_treedata.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/convert_to_treedata.Rd -------------------------------------------------------------------------------- /man/data-hmp_aerobiosis_small.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/data-hmp_aerobiosis_small.Rd -------------------------------------------------------------------------------- /man/data-kostic2012crc.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/data-kostic2012crc.Rd -------------------------------------------------------------------------------- /man/data-test_otu_data.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/data-test_otu_data.Rd -------------------------------------------------------------------------------- /man/diffAnalysisClass-class.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/diffAnalysisClass-class.Rd -------------------------------------------------------------------------------- /man/diff_analysis.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/diff_analysis.Rd -------------------------------------------------------------------------------- /man/dr_extract.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/dr_extract.Rd -------------------------------------------------------------------------------- /man/drop_taxa.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/drop_taxa.Rd -------------------------------------------------------------------------------- /man/extract_binary_offspring.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/extract_binary_offspring.Rd -------------------------------------------------------------------------------- /man/generalizedFC.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/generalizedFC.Rd -------------------------------------------------------------------------------- /man/get_NRI_NTI-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/get_NRI_NTI-methods.Rd -------------------------------------------------------------------------------- /man/get_alltaxadf.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/get_alltaxadf.Rd -------------------------------------------------------------------------------- /man/get_alphaindex.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/get_alphaindex.Rd -------------------------------------------------------------------------------- /man/get_clust.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/get_clust.Rd -------------------------------------------------------------------------------- /man/get_coord.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/get_coord.Rd -------------------------------------------------------------------------------- /man/get_count.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/get_count.Rd -------------------------------------------------------------------------------- /man/get_dist.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/get_dist.Rd -------------------------------------------------------------------------------- /man/get_mean_median.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/get_mean_median.Rd -------------------------------------------------------------------------------- /man/get_pca.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/get_pca.Rd -------------------------------------------------------------------------------- /man/get_pcoa.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/get_pcoa.Rd -------------------------------------------------------------------------------- /man/get_pvalue.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/get_pvalue.Rd -------------------------------------------------------------------------------- /man/get_rarecurve.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/get_rarecurve.Rd -------------------------------------------------------------------------------- /man/get_sampledflist.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/get_sampledflist.Rd -------------------------------------------------------------------------------- /man/get_taxadf.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/get_taxadf.Rd -------------------------------------------------------------------------------- /man/get_upset.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/get_upset.Rd -------------------------------------------------------------------------------- /man/get_varct.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/get_varct.Rd -------------------------------------------------------------------------------- /man/get_vennlist.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/get_vennlist.Rd -------------------------------------------------------------------------------- /man/ggbartax.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/ggbartax.Rd -------------------------------------------------------------------------------- /man/ggbox.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/ggbox.Rd -------------------------------------------------------------------------------- /man/ggclust.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/ggclust.Rd -------------------------------------------------------------------------------- /man/ggdiffbox.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/ggdiffbox.Rd -------------------------------------------------------------------------------- /man/ggdiffclade.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/ggdiffclade.Rd -------------------------------------------------------------------------------- /man/ggdifftaxbar.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/ggdifftaxbar.Rd -------------------------------------------------------------------------------- /man/ggeffectsize.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/ggeffectsize.Rd -------------------------------------------------------------------------------- /man/ggordpoint.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/ggordpoint.Rd -------------------------------------------------------------------------------- /man/ggrarecurve.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/ggrarecurve.Rd -------------------------------------------------------------------------------- /man/mouse.time.mpse.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mouse.time.mpse.Rd -------------------------------------------------------------------------------- /man/mp_adonis-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_adonis-methods.Rd -------------------------------------------------------------------------------- /man/mp_aggregate-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_aggregate-methods.Rd -------------------------------------------------------------------------------- /man/mp_aggregate_clade-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_aggregate_clade-methods.Rd -------------------------------------------------------------------------------- /man/mp_anosim-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_anosim-methods.Rd -------------------------------------------------------------------------------- /man/mp_balance_clade-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_balance_clade-methods.Rd -------------------------------------------------------------------------------- /man/mp_cal_abundance-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_cal_abundance-methods.Rd -------------------------------------------------------------------------------- /man/mp_cal_alpha-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_cal_alpha-methods.Rd -------------------------------------------------------------------------------- /man/mp_cal_cca-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_cal_cca-methods.Rd -------------------------------------------------------------------------------- /man/mp_cal_clust-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_cal_clust-methods.Rd -------------------------------------------------------------------------------- /man/mp_cal_dca-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_cal_dca-methods.Rd -------------------------------------------------------------------------------- /man/mp_cal_dist-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_cal_dist-methods.Rd -------------------------------------------------------------------------------- /man/mp_cal_divergence-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_cal_divergence-methods.Rd -------------------------------------------------------------------------------- /man/mp_cal_nmds-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_cal_nmds-methods.Rd -------------------------------------------------------------------------------- /man/mp_cal_pca-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_cal_pca-methods.Rd -------------------------------------------------------------------------------- /man/mp_cal_pcoa-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_cal_pcoa-methods.Rd -------------------------------------------------------------------------------- /man/mp_cal_pd_metric-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_cal_pd_metric-methods.Rd -------------------------------------------------------------------------------- /man/mp_cal_rarecurve-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_cal_rarecurve-methods.Rd -------------------------------------------------------------------------------- /man/mp_cal_rda-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_cal_rda-methods.Rd -------------------------------------------------------------------------------- /man/mp_cal_upset-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_cal_upset-methods.Rd -------------------------------------------------------------------------------- /man/mp_cal_venn-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_cal_venn-methods.Rd -------------------------------------------------------------------------------- /man/mp_decostand-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_decostand-methods.Rd -------------------------------------------------------------------------------- /man/mp_diff_analysis-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_diff_analysis-methods.Rd -------------------------------------------------------------------------------- /man/mp_diff_clade-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_diff_clade-methods.Rd -------------------------------------------------------------------------------- /man/mp_dmn-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_dmn-methods.Rd -------------------------------------------------------------------------------- /man/mp_dmngroup-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_dmngroup-methods.Rd -------------------------------------------------------------------------------- /man/mp_envfit-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_envfit-methods.Rd -------------------------------------------------------------------------------- /man/mp_extract_abundance-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_extract_abundance-methods.Rd -------------------------------------------------------------------------------- /man/mp_extract_assays-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_extract_assays-methods.Rd -------------------------------------------------------------------------------- /man/mp_extract_dist-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_extract_dist-methods.Rd -------------------------------------------------------------------------------- /man/mp_extract_feature-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_extract_feature-methods.Rd -------------------------------------------------------------------------------- /man/mp_extract_internal_attr-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_extract_internal_attr-methods.Rd -------------------------------------------------------------------------------- /man/mp_extract_rarecurve-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_extract_rarecurve-methods.Rd -------------------------------------------------------------------------------- /man/mp_extract_refseq-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_extract_refseq-methods.Rd -------------------------------------------------------------------------------- /man/mp_extract_sample-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_extract_sample-methods.Rd -------------------------------------------------------------------------------- /man/mp_extract_taxonomy-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_extract_taxonomy-methods.Rd -------------------------------------------------------------------------------- /man/mp_extract_tree-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_extract_tree-methods.Rd -------------------------------------------------------------------------------- /man/mp_filter_taxa-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_filter_taxa-methods.Rd -------------------------------------------------------------------------------- /man/mp_fortify.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_fortify.Rd -------------------------------------------------------------------------------- /man/mp_import_biom.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_import_biom.Rd -------------------------------------------------------------------------------- /man/mp_import_humann_regroup.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_import_humann_regroup.Rd -------------------------------------------------------------------------------- /man/mp_import_metaphlan.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_import_metaphlan.Rd -------------------------------------------------------------------------------- /man/mp_import_qiime.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_import_qiime.Rd -------------------------------------------------------------------------------- /man/mp_mantel-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_mantel-methods.Rd -------------------------------------------------------------------------------- /man/mp_mrpp-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_mrpp-methods.Rd -------------------------------------------------------------------------------- /man/mp_plot_abundance-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_plot_abundance-methods.Rd -------------------------------------------------------------------------------- /man/mp_plot_alpha-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_plot_alpha-methods.Rd -------------------------------------------------------------------------------- /man/mp_plot_diff_boxplot-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_plot_diff_boxplot-methods.Rd -------------------------------------------------------------------------------- /man/mp_plot_diff_cladogram.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_plot_diff_cladogram.Rd -------------------------------------------------------------------------------- /man/mp_plot_diff_manhattan-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_plot_diff_manhattan-methods.Rd -------------------------------------------------------------------------------- /man/mp_plot_diff_res-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_plot_diff_res-methods.Rd -------------------------------------------------------------------------------- /man/mp_plot_dist-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_plot_dist-methods.Rd -------------------------------------------------------------------------------- /man/mp_plot_ord-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_plot_ord-methods.Rd -------------------------------------------------------------------------------- /man/mp_plot_rarecurve-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_plot_rarecurve-methods.Rd -------------------------------------------------------------------------------- /man/mp_plot_upset-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_plot_upset-methods.Rd -------------------------------------------------------------------------------- /man/mp_plot_venn-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_plot_venn-methods.Rd -------------------------------------------------------------------------------- /man/mp_rrarefy-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_rrarefy-methods.Rd -------------------------------------------------------------------------------- /man/mp_select_as_tip-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_select_as_tip-methods.Rd -------------------------------------------------------------------------------- /man/mp_stat_taxa-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/mp_stat_taxa-methods.Rd -------------------------------------------------------------------------------- /man/multi_compare.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/multi_compare.Rd -------------------------------------------------------------------------------- /man/ordplotClass-class.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/ordplotClass-class.Rd -------------------------------------------------------------------------------- /man/pcasample-class.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/pcasample-class.Rd -------------------------------------------------------------------------------- /man/pcoa-class.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/pcoa-class.Rd -------------------------------------------------------------------------------- /man/prcomp-class.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/prcomp-class.Rd -------------------------------------------------------------------------------- /man/print.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/print.Rd -------------------------------------------------------------------------------- /man/read_qza.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/read_qza.Rd -------------------------------------------------------------------------------- /man/reexports.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/reexports.Rd -------------------------------------------------------------------------------- /man/scale_fill_diff_cladogram.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/scale_fill_diff_cladogram.Rd -------------------------------------------------------------------------------- /man/set_diff_boxplot_color.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/set_diff_boxplot_color.Rd -------------------------------------------------------------------------------- /man/set_scale_theme.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/set_scale_theme.Rd -------------------------------------------------------------------------------- /man/show-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/show-methods.Rd -------------------------------------------------------------------------------- /man/split_data.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/split_data.Rd -------------------------------------------------------------------------------- /man/split_str_to_list.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/split_str_to_list.Rd -------------------------------------------------------------------------------- /man/theme_taxbar.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/man/theme_taxbar.Rd -------------------------------------------------------------------------------- /tests/testthat.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/tests/testthat.R -------------------------------------------------------------------------------- /tests/testthat/test_balance_clade.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/tests/testthat/test_balance_clade.R -------------------------------------------------------------------------------- /tests/testthat/test_convert.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/tests/testthat/test_convert.R -------------------------------------------------------------------------------- /tests/testthat/test_extractargs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/tests/testthat/test_extractargs.R -------------------------------------------------------------------------------- /tests/testthat/test_gettax.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/tests/testthat/test_gettax.R -------------------------------------------------------------------------------- /tests/testthat/test_getvennlist.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/tests/testthat/test_getvennlist.R -------------------------------------------------------------------------------- /tests/testthat/test_multicompare.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/tests/testthat/test_multicompare.R -------------------------------------------------------------------------------- /vignettes/MicrobiotaProcess.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/vignettes/MicrobiotaProcess.Rmd -------------------------------------------------------------------------------- /vignettes/mp-design.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/vignettes/mp-design.png -------------------------------------------------------------------------------- /vignettes/mpse.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/vignettes/mpse.png -------------------------------------------------------------------------------- /vignettes/refer.bib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/MicrobiotaProcess/HEAD/vignettes/refer.bib --------------------------------------------------------------------------------