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

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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

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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

vallenderlab/MicrobiomeR documentation built on Aug. 30, 2019, 11:24 p.m.