Man pages for jeffkimbrel/jakR
jakR Miscellaneous Scripts
| 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 |
| illumina_codes | Get Illumina machine and flow cell code from run id |
| 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 |
