Files in HuaZou/MicrobiomeAnalysis
Data analysis toolkits in metagenomics
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE.md
MicrobiomeAnalysis.Rproj
NAMESPACE
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/sysdata.rda
R/utilities.R
R/utilities_lefse.R
R/utilities_statistics.R
README.Rmd
README.md
_pkgdown.yml
codecov.yml
data-raw/available_ranks.R
data-raw/data.R
data/Zeybel_2022_gut.rda
data/Zeybel_2022_gut_paired.rda
data/Zeybel_2022_metabolite.rda
data/Zeybel_2022_metabolite_paired.rda
data/Zeybel_2022_oral.rda
data/Zeybel_2022_oral_paired.rda
data/Zeybel_2022_protein.rda
data/Zeybel_2022_protein_paired.rda
data/caporaso.rda
data/ecam.rda
data/enterotypes_arumugam.rda
inst/CITATION
inst/extdata/MetaPhlAn/metaphlan_test.txt
inst/extdata/MetaPhlAn/sample_test.txt
inst/extdata/dada2_samdata.txt
inst/extdata/dada2_seqtab.rds
inst/extdata/dada2_taxtab.rds
inst/extdata/path_abun_unstrat_descrip.tsv.gz
inst/extdata/picrust2_metadata.tsv
inst/extdata/refseq.qza
inst/extdata/sample-metadata.tsv
inst/extdata/table.qza
inst/extdata/taxonomy.qza
inst/extdata/tree.qza
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/figures/Schematic.png
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
vignettes/reference.bib
