Files in OxfordCMS/OCMSutility
Utility functions for OCMS
.gitignore
DESCRIPTION
Makefile
NAMESPACE
R/OCMSutility-package.R
R/adjust_mat_pval.R
R/aggregateCount.R
R/aggregate_count.R
R/alpha_diversity.R
R/annotated_dendrogram.R
R/asv_example.R
R/bcdissimilarity.R
R/clr.R
R/compare_cor_ci.R
R/convert_platemap.R
R/dissimilarity.R
R/dss_example.R
R/featurebox.R
R/filterFeature.R
R/filter_feature.R
R/geom_remove.R
R/getPalette.R
R/get_palette.R
R/get_shortnames.R
R/metadata_sparsity.R
R/metfile_init.R
R/nsample_by_var.R
R/pca_by_var.R
R/pcoa_by_var.R
R/plotPCA.R
R/plotPCoA.R
R/plotSunburst.R
R/plot_pca.R
R/plot_pcoa.R
R/prevalence_abundance.R
R/rarefaction.R
R/reannotateTax.R
R/reannotate_tax.R
R/relab.R
R/stacked_barchart.R
R/sym_mat2df.R
R/top_taxa.R
R/truePosRate.R
R/true_pos_rate.R
R/zymobiomics.R
README.md
data-raw/dss_db
data-raw/dss_example.R
data-raw/dss_metadata.tsv
data-raw/tax_example.R
data-raw/zymobiomics.R
data/asv_example.RData
data/dss_example.RData
data/zymobiomics.rda
doc/OCMSutility.R
doc/OCMSutility.Rmd
doc/OCMSutility.html
man/OCMSutility-package.Rd
man/adjust_mat_pval.Rd
man/aggregateCount.Rd
man/aggregate_count.Rd
man/alpha_diversity.Rd
man/annotated_dendrogram.Rd
man/asv_example.Rd
man/bcdissimilarity.Rd
man/clr.Rd
man/compare_cor_ci.Rd
man/convert_platemap.Rd
man/dissimilarity.Rd
man/dss_example.Rd
man/featurebox.Rd
man/figures/lifecycle-archived.svg
man/figures/lifecycle-defunct.svg
man/figures/lifecycle-deprecated.svg
man/figures/lifecycle-experimental.svg
man/figures/lifecycle-maturing.svg
man/figures/lifecycle-questioning.svg
man/figures/lifecycle-soft-deprecated.svg
man/figures/lifecycle-stable.svg
man/figures/lifecycle-superseded.svg
man/filterFeature.Rd
man/filter_feature.Rd
man/getPalette.Rd
man/getVE.Rd
man/get_palette.Rd
man/get_shortnames.Rd
man/hello.Rd
man/metadata_sparsity.Rd
man/metfile_init.Rd
man/nsample_by_var.Rd
man/pca_by_var.Rd
man/pcoa_by_var.Rd
man/plotPCA.Rd
man/plotPCoA.Rd
man/plotSunburst.Rd
man/plot_pca.Rd
man/plot_pcoa.Rd
man/prevalence_abundance.Rd
man/rarefaction.Rd
man/reannotateTax.Rd
man/reannotate_tax.Rd
man/relab.Rd
man/remove_geom.Rd
man/stacked_barchart.Rd
man/sym_mat2df.Rd
man/top_taxa.Rd
man/truePosRate.Rd
man/true_pos_rate.Rd
man/zymobiomics.Rd
vignettes/OCMSutility.Rmd
vignettes/OCMSutility.md
vignettes/OCMSutility_files/figure-markdown_strict/annotated-dendrogram-1.png
vignettes/OCMSutility_files/figure-markdown_strict/annotated-dendrogram-2.png
vignettes/OCMSutility_files/figure-markdown_strict/bcdissimilarity-1.png
vignettes/OCMSutility_files/figure-markdown_strict/bcdissimilarity-2.png
vignettes/OCMSutility_files/figure-markdown_strict/dissimilarity-1.png
vignettes/OCMSutility_files/figure-markdown_strict/featurebox-1.png
vignettes/OCMSutility_files/figure-markdown_strict/featurebox_colour-1.png
vignettes/OCMSutility_files/figure-markdown_strict/getPalette-1.png
vignettes/OCMSutility_files/figure-markdown_strict/get_palette-1.png
vignettes/OCMSutility_files/figure-markdown_strict/pca_by_var-1.png
vignettes/OCMSutility_files/figure-markdown_strict/pca_by_var-2.png
vignettes/OCMSutility_files/figure-markdown_strict/pca_by_var-3.png
vignettes/OCMSutility_files/figure-markdown_strict/pca_by_var-4.png
vignettes/OCMSutility_files/figure-markdown_strict/pca_by_var-5.png
vignettes/OCMSutility_files/figure-markdown_strict/pca_by_var-6.png
vignettes/OCMSutility_files/figure-markdown_strict/pcoa_by_var-1.png
vignettes/OCMSutility_files/figure-markdown_strict/pcoa_by_var-2.png
vignettes/OCMSutility_files/figure-markdown_strict/pcoa_by_var-3.png
vignettes/OCMSutility_files/figure-markdown_strict/pcoa_by_var-4.png
vignettes/OCMSutility_files/figure-markdown_strict/pcoa_by_var-5.png
vignettes/OCMSutility_files/figure-markdown_strict/pcoa_by_var-6.png
vignettes/OCMSutility_files/figure-markdown_strict/plotPCA-1.png
vignettes/OCMSutility_files/figure-markdown_strict/plotPCA-2.png
vignettes/OCMSutility_files/figure-markdown_strict/plotPCoA-1.png
vignettes/OCMSutility_files/figure-markdown_strict/plotPCoA-2.png
vignettes/OCMSutility_files/figure-markdown_strict/plot_pca-1.png
vignettes/OCMSutility_files/figure-markdown_strict/plot_pca-2.png
vignettes/OCMSutility_files/figure-markdown_strict/plot_pcoa-1.png
vignettes/OCMSutility_files/figure-markdown_strict/plot_pcoa-2.png
vignettes/OCMSutility_files/figure-markdown_strict/prevalence_abundance-1.png
vignettes/OCMSutility_files/figure-markdown_strict/rarefaction-1.png
vignettes/OCMSutility_files/figure-markdown_strict/rarefaction-2.png
vignettes/OCMSutility_files/figure-markdown_strict/remove_geom-1.png
vignettes/OCMSutility_files/figure-markdown_strict/remove_geom-2.png
vignettes/OCMSutility_files/figure-markdown_strict/stacked barchart-1.png
vignettes/OCMSutility_files/figure-markdown_strict/truPosRate-1.png
vignettes/OCMSutility_files/figure-markdown_strict/true_pos_rate-1.png
