Files in vallenderlab/MicrobiomeR
Analyze Microbiome Data
.Rbuildignore
.github/CODE_OF_CONDUCT.md
.github/CONTRIBUTING.md
.github/ISSUE_TEMPLATE.md
.github/PULL_REQUEST_TEMPLATE.md
.gitignore
.travis.yml
DESCRIPTION
LICENSE
MicrobiomeR.Rproj
NAMESPACE
NEWS.md
R/MicrobiomeR-package.R
R/alpha-diversity.R
R/barplot.R
R/correlation-plot.R
R/data.R
R/heat-tree.R
R/metacoder-formatting.R
R/metacoder.R
R/ordination.R
R/package.R
R/palettes.R
R/permanova.R
R/phyloseq.R
R/utils-pipe.R
R/utils.R
README.md
_pkgdown.yml
codecov.yml
data/phyloseq_silva_2.rda
data/phyloseq_silva_3.rda
data/raw_silva_2.rda
data/raw_silva_3.rda
docs/CNAME
docs/CODE_OF_CONDUCT.html
docs/CONTRIBUTING.html
docs/ISSUE_TEMPLATE.html
docs/LICENSE-text.html
docs/PULL_REQUEST_TEMPLATE.html
docs/articles/Microbiome-Workflow.png
docs/articles/about.html
docs/articles/about_files/Proj4Leaflet-1.0.1/proj4-compressed.js
docs/articles/about_files/Proj4Leaflet-1.0.1/proj4leaflet.js
docs/articles/about_files/figure-html/unnamed-chunk-1-1.png
docs/articles/about_files/figure-html/unnamed-chunk-1-2.png
docs/articles/about_files/htmlwidgets-1.3/htmlwidgets.js
docs/articles/about_files/jquery-1.12.4/jquery.min.js
docs/articles/about_files/leaflet-1.3.1/images/layers-2x.png
docs/articles/about_files/leaflet-1.3.1/images/layers.png
docs/articles/about_files/leaflet-1.3.1/images/marker-icon-2x.png
docs/articles/about_files/leaflet-1.3.1/images/marker-icon.png
docs/articles/about_files/leaflet-1.3.1/images/marker-shadow.png
docs/articles/about_files/leaflet-1.3.1/leaflet.css
docs/articles/about_files/leaflet-1.3.1/leaflet.js
docs/articles/about_files/leaflet-binding-2.0.2/leaflet.js
docs/articles/about_files/leafletfix-1.0.0/leafletfix.css
docs/articles/about_files/rstudio_leaflet-1.3.1/images/1px.png
docs/articles/about_files/rstudio_leaflet-1.3.1/rstudio_leaflet.css
docs/articles/analysis.html
docs/articles/analysis_files/figure-html/unnamed-chunk-10-1.png
docs/articles/analysis_files/figure-html/unnamed-chunk-11-1.png
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docs/articles/analysis_files/figure-html/unnamed-chunk-9-5.png
docs/articles/analysis_files/figure-html/unnamed-chunk-9-6.png
docs/articles/color-palettes.html
docs/articles/color-palettes_files/figure-html/unnamed-chunk-1-1.png
docs/articles/color-palettes_files/figure-html/unnamed-chunk-1-2.png
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docs/articles/color-palettes_files/figure-html/unnamed-chunk-4-1.png
docs/articles/color-palettes_files/figure-html/unnamed-chunk-5-1.png
docs/articles/data-wrangling.html
docs/articles/filtering.html
docs/articles/index.html
docs/articles/introduction.html
docs/articles/paper.html
docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/extra.css
docs/index.html
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/MicrobiomeR.html
docs/reference/MicrobiomeR_Formats.html
docs/reference/MicrobiomeR_Workflow.html
docs/reference/agglomerate_metacoder.html
docs/reference/agglomerate_taxmap.html
docs/reference/alpha_diversity_measures.html
docs/reference/alpha_diversity_plot.html
docs/reference/as_MicrobiomeR_format.html
docs/reference/as_analyzed_format.html
docs/reference/as_basic_format.html
docs/reference/as_custom_format.html
docs/reference/as_phyloseq_format.html
docs/reference/as_raw_format.html
docs/reference/combination_palette.html
docs/reference/convert_proportions.html
docs/reference/correlation_data.html
docs/reference/correlation_plot.html
docs/reference/correlation_plots.html
docs/reference/cov_filter.html
docs/reference/create_metacoder.html
docs/reference/create_phyloseq.html
docs/reference/create_pub_table.html
docs/reference/create_taxmap.html
docs/reference/get_alpha_diversity.html
docs/reference/get_alpha_diversity_measures.html
docs/reference/get_color_palette.html
docs/reference/get_correlation_data.html
docs/reference/get_correlation_plots.html
docs/reference/get_distance_methods.html
docs/reference/get_heat_tree_parameters.html
docs/reference/get_heat_tree_plots.html
docs/reference/get_output_dir.html
docs/reference/get_phyloseq_obj.html
docs/reference/get_plot_limits.html
docs/reference/get_treatment_matrix.html
docs/reference/heat_tree_parameters.html
docs/reference/heat_tree_plots.html
docs/reference/index.html
docs/reference/is_analyzed_format.html
docs/reference/is_basic_format.html
docs/reference/is_phyloseq_format.html
docs/reference/is_raw_format.html
docs/reference/melt_metacoder.html
docs/reference/melt_taxmap.html
docs/reference/metacoder_comp_func_1.html
docs/reference/mkdir.html
docs/reference/object_handler.html
docs/reference/order_metacoder_data.html
docs/reference/ordination_plot.html
docs/reference/ordination_plots.html
docs/reference/otu_id_filter.html
docs/reference/otu_prevalence_filter.html
docs/reference/otu_proportion_filter.html
docs/reference/otutax_to_dataframe.html
docs/reference/output_dir.html
docs/reference/parse_taxonomy_greengenes2.html
docs/reference/parse_taxonomy_silva.html
docs/reference/parse_taxonomy_silva_128.html
docs/reference/permanova.html
docs/reference/phyloseq_greengenes.html
docs/reference/phyloseq_silva.html
docs/reference/phyloseq_silva_2.html
docs/reference/phyloseq_silva_3.html
docs/reference/phyloseq_to_tibble.html
docs/reference/pick_new_outgroup.html
docs/reference/pipe.html
docs/reference/plot_limits.html
docs/reference/preprocess_phyloseq.html
docs/reference/raw_greengenes.html
docs/reference/raw_silva.html
docs/reference/raw_silva_2.html
docs/reference/raw_silva_3.html
docs/reference/remove_ambiguous_taxa.html
docs/reference/root_by_longest_edge.html
docs/reference/root_phyloseq_tree.html
docs/reference/sample_id_filter.html
docs/reference/save_alpha_diversity_plots.html
docs/reference/save_barplot.html
docs/reference/save_correlation_plots.html
docs/reference/save_heat_tree_plots.html
docs/reference/save_ordination_plots.html
docs/reference/save_stacked_barplot.html
docs/reference/save_stacked_barplots.html
docs/reference/save_top_coefficients_barplot.html
docs/reference/scico_palette.html
docs/reference/stacked_barplot.html
docs/reference/stacked_barplots.html
docs/reference/taxa_prevalence_filter.html
docs/reference/taxon_id_filter.html
docs/reference/top_coefficients_barplot.html
docs/reference/transform_metacoder.html
docs/reference/transformer.html
docs/reference/transposer.html
docs/reference/treatment_matrix.html
docs/reference/validate_MicrobiomeR_format.html
docs/reference/viridis_magma_palette.html
docs/reference/viridis_palette.html
docs/reference/vlookup.html
docs/reference/which_format.html
docs/sitemap.xml
inst/extdata/greengenes.tre
inst/extdata/greengenes_OTU.biom
inst/extdata/nephele_metadata2.txt
inst/extdata/nephele_metadata3.txt
inst/extdata/process_list.yml
inst/extdata/silva.tre
inst/extdata/silva_OTU.biom
inst/paper/Microbiome-Workflow.png
inst/paper/paper.bib
inst/paper/paper.md
man/MicrobiomeR.Rd
man/MicrobiomeR_Formats.Rd
man/MicrobiomeR_Workflow.Rd
man/agglomerate_taxmap.Rd
man/alpha_diversity_measures.Rd
man/alpha_diversity_plot.Rd
man/as_MicrobiomeR_format.Rd
man/as_analyzed_format.Rd
man/as_basic_format.Rd
man/as_custom_format.Rd
man/as_phyloseq_format.Rd
man/as_raw_format.Rd
man/combination_palette.Rd
man/convert_proportions.Rd
man/correlation_data.Rd
man/correlation_plot.Rd
man/correlation_plots.Rd
man/cov_filter.Rd
man/create_phyloseq.Rd
man/create_pub_table.Rd
man/create_taxmap.Rd
man/figures/logo.png
man/get_color_palette.Rd
man/heat_tree_parameters.Rd
man/heat_tree_plots.Rd
man/is_analyzed_format.Rd
man/is_basic_format.Rd
man/is_phyloseq_format.Rd
man/is_raw_format.Rd
man/melt_taxmap.Rd
man/metacoder_comp_func_1.Rd
man/order_metacoder_data.Rd
man/ordination_plot.Rd
man/ordination_plots.Rd
man/otu_id_filter.Rd
man/otu_prevalence_filter.Rd
man/otu_proportion_filter.Rd
man/output_dir.Rd
man/parse_taxonomy_silva_128.Rd
man/permanova.Rd
man/phyloseq_silva_2.Rd
man/phyloseq_silva_3.Rd
man/pick_new_outgroup.Rd
man/pipe.Rd
man/plot_limits.Rd
man/raw_silva_2.Rd
man/raw_silva_3.Rd
man/root_by_longest_edge.Rd
man/root_phyloseq_tree.Rd
man/sample_id_filter.Rd
man/save_alpha_diversity_plots.Rd
man/save_correlation_plots.Rd
man/save_heat_tree_plots.Rd
man/save_ordination_plots.Rd
man/save_stacked_barplots.Rd
man/save_top_coefficients_barplot.Rd
man/scico_palette.Rd
man/stacked_barplot.Rd
man/stacked_barplots.Rd
man/taxa_prevalence_filter.Rd
man/taxon_id_filter.Rd
man/top_coefficients_barplot.Rd
man/transformer.Rd
man/transposer.Rd
man/treatment_matrix.Rd
man/validate_MicrobiomeR_format.Rd
man/viridis_magma_palette.Rd
man/viridis_palette.Rd
man/vlookup.Rd
man/which_format.Rd
pkgdown/extra.css
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
tests/testthat.R
tests/testthat/test-alpha-diversity.R
tests/testthat/test-barplot.R
tests/testthat/test-correlation-plot.R
tests/testthat/test-heat-tree.R
tests/testthat/test-metacoder-formatting.R
tests/testthat/test-metacoder.R
tests/testthat/test-ordination.R
tests/testthat/test-palettes.R
tests/testthat/test-permanova.R
tests/testthat/test-phyloseq.R
tests/testthat/test-utils.R
vignettes/.gitignore
vignettes/Microbiome-Workflow.png
vignettes/about.Rmd
vignettes/analysis.Rmd
vignettes/color-palettes.Rmd
vignettes/data-wrangling.Rmd
vignettes/filtering.Rmd
vignettes/introduction.Rmd
vignettes/paper.Rmd
vignettes/paper.bib
