Files in hiplot/animalcules
Interactive microbiome analysis toolkit
.Rbuildignore
.gitignore
CONDUCT.md
DESCRIPTION
Dockerfile
LICENSE
NAMESPACE
R/alpha_div_boxplot.R
R/alpha_div_test.R
R/animalcules-package.R
R/differential_abundance.R
R/dimred_pca.R
R/dimred_pcoa.R
R/dimred_tsne.R
R/dimred_umap.R
R/diversities.R
R/diversities_help.R
R/diversity_beta_boxplot.R
R/diversity_beta_heatmap.R
R/diversity_beta_test.R
R/do_alpha_div_test.R
R/filter_categorize.R
R/filter_summary_bar_density.R
R/filter_summary_pie_box.R
R/find_biomarker.R
R/find_taxon_mat.R
R/find_taxonomy.R
R/find_taxonomy_300.R
R/gini_simpson.R
R/grep_tid.R
R/inverse_simpson.R
R/read_pathoscope_data.R
R/relabu_barplot.R
R/relabu_boxplot.R
R/relabu_heatmap.R
R/runApp.R
R/shannon.R
R/simpson_index.R
R/utils.R
R/write_to_biom.R
README.md
codecov.yml
inst/extdata/MAE.rds
inst/extdata/TB_example_dataset.rds
inst/extdata/animalcules.rds
inst/extdata/asthma_example_dataset.rds
inst/extdata/biom_example.rds
inst/extdata/toy_data.rds
inst/script/extdata.R
inst/shiny/app.R
inst/shiny/server/server_01_upload.R
inst/shiny/server/server_02_filter.R
inst/shiny/server/server_03_relabu.R
inst/shiny/server/server_04_diversity.R
inst/shiny/server/server_05_dimred.R
inst/shiny/server/server_06_differential.R
inst/shiny/server/server_07_biomarker.R
inst/shiny/ui/ui_01_upload.R
inst/shiny/ui/ui_02_filter.R
inst/shiny/ui/ui_03_relabu.R
inst/shiny/ui/ui_04_diversity.R
inst/shiny/ui/ui_05_dimred.R
inst/shiny/ui/ui_06_differential.R
inst/shiny/ui/ui_07_biomarker.R
inst/shiny/utils/helpers.R
inst/shiny/utils/server_util.R
inst/shiny/utils/ui_util.R
inst/shiny/www/ajax-loader-bar.gif
inst/shiny/www/animalcules_logo.png
inst/shiny/www/bootstrap.min.css
inst/shiny/www/bu_bioinfo_logo.png
inst/shiny/www/bu_logo.PNG
inst/shiny/www/cbm.PNG
inst/shiny/www/count_table_example.png
inst/shiny/www/footer.html
man/alpha_div_boxplot.Rd
man/alpha_div_test.Rd
man/animalcules-package.Rd
man/counts_to_logcpm.Rd
man/counts_to_relabu.Rd
man/df_char_to_factor.Rd
man/differential_abundance.Rd
man/dimred_pca.Rd
man/dimred_pcoa.Rd
man/dimred_tsne.Rd
man/dimred_umap.Rd
man/diversities.Rd
man/diversities_help.Rd
man/diversity_beta_boxplot.Rd
man/diversity_beta_heatmap.Rd
man/diversity_beta_test.Rd
man/do_alpha_div_test.Rd
man/filter_categorize.Rd
man/filter_summary_bar_density.Rd
man/filter_summary_pie_box.Rd
man/find_biomarker.Rd
man/find_taxon_mat.Rd
man/find_taxonomy.Rd
man/find_taxonomy_300.Rd
man/gini_simpson.Rd
man/grep_tid.Rd
man/inverse_simpson.Rd
man/is_categorical.Rd
man/is_integer0.Rd
man/is_integer1.Rd
man/mae_pick_organisms.Rd
man/mae_pick_samples.Rd
man/pct2str.Rd
man/percent.Rd
man/read_pathoscope_data.Rd
man/relabu_barplot.Rd
man/relabu_boxplot.Rd
man/relabu_heatmap.Rd
man/run_animalcules.Rd
man/shannon.Rd
man/simpson_index.Rd
man/upsample_counts.Rd
man/write_to_biom.Rd
pkgdown/_pkgdown.yml
tests/testthat.R
tests/testthat/test-examples.R
vignettes/animalcules.Rmd
vignettes/rmd/abundance.Rmd
vignettes/rmd/biomarker.Rmd
vignettes/rmd/differential.Rmd
vignettes/rmd/dimension.Rmd
vignettes/rmd/diversity.Rmd
vignettes/rmd/summary.Rmd
vignettes/rmd/upload.Rmd
