Files in HuaZou/MicrobiomeAnalysis

Data analysis toolkits in metagenomics

LICENSE.md NEWS.md R/AllClasses.R R/AllGenerics.R R/Alldata.R R/assignment_methods.R R/confounder.R R/da_aldex.R R/da_all.R R/da_ancom.R R/da_ancombc.R R/da_deseq2.R R/da_edgeR.R R/da_lefse.R R/da_limma_voom.R R/da_metabolome.R R/da_metagenomeSeq.R R/da_multiple_groups.R R/da_simple_statistic.R R/da_supervised_leaning.R R/da_two_groups.R R/extract_methods.R R/gv_ANOSIM.R R/gv_MANTEL.R R/gv_MRPP.R R/gv_PERMANOVA.R R/gv_betadisper.R R/gv_distance.R R/gv_diversity.R R/gv_ordination.R R/plot_ord_scatter.R R/plot_volcano_scatter.R R/process_abundances_methods.R R/process_aggregate_taxa.R R/process_filter_abundance.R R/process_import_SE.R R/process_import_dada2.R R/process_import_qiime2.R R/process_imputation.R R/process_normalization.R R/process_summarize_taxa.R R/process_transform.R R/process_trim_prevalence.R R/reexports.R R/subset_marker.R R/utilities.R R/utilities_lefse.R R/utilities_statistics.R README.Rmd README.md data-raw/available_ranks.R data-raw/data.R man/abundances-methods.Rd man/aggregate_taxa.Rd man/assign-marker_table.Rd man/assign-otu_table.Rd man/calculate_MeanRank_abundance.Rd man/calculate_geometricmean_abundance.Rd man/calculate_mean_abundance.Rd man/calculate_median_abundance.Rd man/calculate_occurrence_taxa.Rd man/check_sample_names.Rd man/confounder.Rd man/data-Zeybel_2022_gut.Rd man/data-Zeybel_2022_gut_paired.Rd man/data-Zeybel_2022_metabolite.Rd man/data-Zeybel_2022_metabolite_paired.Rd man/data-Zeybel_2022_oral.Rd man/data-Zeybel_2022_oral_paired.Rd man/data-Zeybel_2022_protein.Rd man/data-Zeybel_2022_protein_paired.Rd man/data-caporaso.Rd man/data-ecam.Rd man/data-enterotypes_arumugam.Rd man/default_color.Rd man/extract-methods.Rd man/figures/MicrobiomeAnalysis.pdf man/filter_abundance.Rd man/get_GUniFrac.Rd man/get_alphaindex.Rd man/get_eigValue.Rd man/import_SE.Rd man/import_dada2.Rd man/import_qiime2.Rd man/impute_abundance.Rd man/insertCol.Rd man/insertRow.Rd man/marker_table-class.Rd man/marker_table-methods.Rd man/microbiomeMarker-class.Rd man/microbiomeMarker.Rd man/nmarker-methods.Rd man/normalize-methods.Rd man/phyloseq2DESeq2.Rd man/phyloseq2edgeR.Rd man/phyloseq2metagenomeSeq.Rd man/plot_ord.Rd man/plot_volcano.Rd man/postHocTest-class.Rd man/postHocTest.Rd man/reexports.Rd man/run_ANOSIM.Rd man/run_CI.Rd man/run_MANTEL.Rd man/run_MRPP.Rd man/run_OddRatio.Rd man/run_PERMANOVA.Rd man/run_STDERR.Rd man/run_aldex.Rd man/run_ancom.Rd man/run_ancombc.Rd man/run_betadisper.Rd man/run_deseq2.Rd man/run_distance.Rd man/run_edger.Rd man/run_group.CI.Rd man/run_group.STDERR.Rd man/run_lefse.Rd man/run_limma_voom.Rd man/run_marker.Rd man/run_metabolomeDA.Rd man/run_metagenomeseq.Rd man/run_ord.Rd man/run_simple_stat.Rd man/run_sl.Rd man/run_summarySE.Rd man/run_test_multiple_groups.Rd man/run_test_two_groups.Rd man/scale_variables.Rd man/subset_marker.Rd man/summarize_taxa.Rd man/transform_abundances.Rd man/trim_prevalence.Rd tests/testthat.R tests/testthat/test_import_qiime2.R vignettes/Introduction.Rmd