all_are_valid_colors | Check if a string contains valid color strings |
drep_extract | Extract dRep genome results |
expand_named_palette | Expanded Color Palette with Names |
fastq_filter_summary_amplicon | Summarize a fastq_filter.py file in amplicon mode |
fastq_filter_summary_meta | Summarize a fastq_filter.py file in metagenome mode |
fastq_info_summary | Summarize a fastq_info file |
format_dt | Format DT Datatable |
get_alpha_diversity | Alpha-Diversity Measures |
getAlphaDiversity | Alpha-Diversity Measures (deprecated) |
get_fts_intervals | Get intervals for a run_fts() dataframe |
get_phylo_diversity | Phylogenetic Diversity Measures |
getPhyloDiversity | Phylogenetic Diversity Measures (deprecated) |
get_phylo_palette | getPhyloPalette |
getSig | getSig |
gt_theme | Web theme for GT |
jak_palettes | Color Palettes |
jak_theme | JAK ggplot theme |
jak_theme_black | JAK ggplot theme |
orthofinder_complete_clusters | Summarize single copy and orthogroups found in all |
orthofinder_summary | Summarize an orthofinder TSV file |
pairwiseAdonis | Calculate Total and Pairwise Adonis Values |
palette_jak | A full-service color palette creator |
permanova | Permanova (adonis) and visualization |
phylo_other | Combine low-abundant taxa into a single category |
plot_distances | Boxplot of Beta-diversity Distances |
plotDistances | plotDistances() (deprecated) |
plot_fts_intervals | Plot intervals for a run_fts() dataframe |
plot_fts_points | Plot points for a run_fts() dataframe |
plotPD | Plot Faith's PD |
run_fts | run_fts |
seqtab_stats | Extract DADA2 seqtab statistics |
show_all_color_palettes | Show all color palettes in the jak_palettes object |
show_color_palette | showColorPalette |
sigCombine | Combine DESeq sigtab contrasts |
summarySE | Calculate Error Bars on a Dataframe |
zeroOTU | Sets ASV abundance values below x to zero |
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