Files in microsud/microbiomeutilities

microbiomeutilities: Utilities for Microbiome Analytics

.Rbuildignore

.Rhistory

.github/workflows/rcmdcheck.yml

.gitignore

.travis.yml

DESCRIPTION

LICENSE

NAMESPACE

R/aggregate_top_taxa2.R R/data.R R/dominant_taxa.R R/extensions.R R/find_samples_taxa.R R/format_to_besthit.R R/get_group_abundances.R R/get_microbiome_data.R R/list_microbiome_data.R R/peak_methods.R R/percent_classified.R R/phy_to_ldf.R R/pkg_checks.R R/pkg_utils.R R/plasticity.R R/plot_abund_prev.R R/plot_alpha_diversities.R R/plot_alpha_rcurve.R R/plot_area.R R/plot_diversity_stats.R R/plot_diversity_stats_utils.R R/plot_listed_taxa.R R/plot_ordination_utils.R R/plot_ordiplot_core.R R/plot_paired_abundances.R R/plot_read_distribution.R R/plot_select_taxa.R R/plot_sphagetti.R R/plot_taxa_boxplot.R R/plot_taxa_composition.R R/plot_taxa_cv.R R/plot_taxa_heatmap.R R/prep_tern_otu.R R/prep_ternary.R R/print_ps.R R/simple_heatmap.R R/sphagetti_utils.R R/taxa_summary.R README.md

data/hmp2.rda

data/zackular2014.rda

docs/404.html

docs/LICENSE-text.html

docs/articles/index.html

docs/articles/microbiomeutilities.html

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docs/articles/microbiomeutilities_ts.html

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docs/authors.html

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docs/pkgdown.css

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docs/reference/abun_summary.html

docs/reference/add_refseq.html

docs/reference/aggregate_top_taxa2.html

docs/reference/dominant_taxa.html

docs/reference/find_samples_taxa.html

docs/reference/format_to_besthit.html

docs/reference/get_group_abundances.html

docs/reference/get_microbiome_data.html

docs/reference/get_tibble.html

docs/reference/hmp2.html

docs/reference/index.html

docs/reference/join_otu_tax.html

docs/reference/list_microbiome_data.html

docs/reference/make_pairs.html

docs/reference/peak-methods.html

docs/reference/percent_classified.html

docs/reference/phy_to_ldf.html

docs/reference/plasticity.html

docs/reference/plot_abund_prev.html

docs/reference/plot_alpha_diversities-1.png

docs/reference/plot_alpha_diversities.html

docs/reference/plot_alpha_rcurve.html

docs/reference/plot_area.html

docs/reference/plot_diversity_stats.html

docs/reference/plot_diversity_with_stats.html

docs/reference/plot_diversity_without_stats.html

docs/reference/plot_listed_taxa.html

docs/reference/plot_ordination_utils.html

docs/reference/plot_ordiplot_core.html

docs/reference/plot_paired_abundances.html

docs/reference/plot_read_distribution-1.png

docs/reference/plot_read_distribution.html

docs/reference/plot_select_taxa.html

docs/reference/plot_spaghetti.html

docs/reference/plot_taxa_boxplot.html

docs/reference/plot_taxa_composition.html

docs/reference/plot_taxa_cv.html

docs/reference/plot_taxa_heatmap-1.png

docs/reference/plot_taxa_heatmap.html

docs/reference/prep_tern_otu.html

docs/reference/prep_ternary.html

docs/reference/print_ps.html

docs/reference/rarefy_util.html

docs/reference/simple_heatmap-1.png

docs/reference/simple_heatmap.html

docs/reference/taxa_distribution-1.png

docs/reference/taxa_distribution.html

docs/reference/taxa_pooler_mcola.html

docs/reference/taxa_summary.html

docs/reference/theme_biome_utils.html

docs/reference/zackular2014.html

docs/sitemap.xml

inst/NEWS

inst/extdata/Mock_report.html

inst/extdata/beta_stats_test.R

inst/extdata/images/Anonymous-work-in-progress.png

inst/extdata/images/Rmarkdown_image.png

inst/extdata/images/boxplot.png

inst/extdata/images/heatmap.png

inst/extdata/microbiomeHD_ref.txt

inst/extdata/microbiomeHD_ref.xlsx

inst/extdata/theme_mutilties.R

inst/extras/build.sh

inst/extras/document.R inst/extras/firstlib.R inst/extras/format_phylo_tax.R inst/extras/hmp2.R

inst/extras/physeq.rds

inst/extras/plot_alpha_diversities.R inst/extras/plot_taxa_boxplot.R inst/extras/plot_taxa_composition.R inst/extras/taxa_summary.R

inst/extras/tern_eg.png

inst/microutility_template.rmd inst/rmarkdown/templates/microbiomeanalysisQC/skeleton/skeleton.Rmd

inst/rmarkdown/templates/microbiomeanalysisQC/template.yaml

man/add_refseq.Rd man/aggregate_top_taxa2.Rd man/dominant_taxa.Rd man/find_samples_taxa.Rd man/format_to_besthit.Rd man/get_group_abundances.Rd man/get_microbiome_data.Rd man/get_tibble.Rd man/hmp2.Rd man/join_otu_tax.Rd man/list_microbiome_data.Rd man/make_pairs.Rd man/peak-methods.Rd man/percent_classified.Rd man/phy_to_ldf.Rd man/plasticity.Rd man/plot_abund_prev.Rd man/plot_alpha_diversities.Rd man/plot_alpha_rcurve.Rd man/plot_area.Rd man/plot_diversity_stats.Rd man/plot_listed_taxa.Rd man/plot_ordination_utils.Rd man/plot_ordiplot_core.Rd man/plot_paired_abundances.Rd man/plot_read_distribution.Rd man/plot_select_taxa.Rd man/plot_spaghetti.Rd man/plot_taxa_boxplot.Rd man/plot_taxa_composition.Rd man/plot_taxa_cv.Rd man/plot_taxa_heatmap.Rd man/prep_tern_otu.Rd man/prep_ternary.Rd man/print_ps.Rd man/rarefy_util.Rd man/simple_heatmap.Rd man/taxa_distribution.Rd man/taxa_pooler_mcola.Rd man/taxa_summary.Rd man/theme_biome_utils.Rd man/zackular2014.Rd

microbiomeutilities-master.Rproj

vignettes/microbiomeutilities.Rmd vignettes/microbiomeutilities_ts.Rmd

microsud/microbiomeutilities documentation built on Nov. 29, 2022, 12:18 a.m.