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Genomics

read_orthogroups()
Import an orthofinder TSV file
orthogroup_list2counts()
Convert an orthogroup list dataframe to a count dataframe

Diversity

get_alpha_diversity()
Alpha-Diversity Measures
get_alpha_S()
Calculate richness (S) and sample depth
get_alpha_simpson()
Calculate Simpson's diversity index and its evenness and inverse
get_alpha_shannon()
Calculate Shannon's diversity index and its evenness and effective number of species (ENS)

Phlyogenetics

get_tip_index()
Get the index of a tip in a tree
get_tip_edges()
Get the edges that lead to a tip

Markdown

file2gfm()
Decorate a file string for gfm markdown in Obsidian
obs2gfm()
Decorate an Obsidian link for gfm markdown

Themes and Colors

jak_theme()
JAK ggplot theme
palette_jak()
A full-service color palette creator
blend_palette()
Blend palette with a color
scale_color_jak_d()
Custom discrete ggplot2 scale color
scale_fill_jak_d()
Custom discrete ggplot2 scale fill
get_color_palette()
Return table of colors for a palette
show_color_palette()
showColorPalette
show_all_color_palettes()
Show all color palettes in the jak_palettes object
get_luminance()
Title
get_text_color()
Title

CARD

card_parse()
Parse CARD database JSON file
card_ab_info()
Get information about an antibiotic
card_gene_info()
Get antibiotic information about a gene
card_gene2ab()
Get gene information about an antibiotic
card_ab2gene()
Get gene information about an antibiotic

fastq

fastq_info_summary()
Summarize a fastq_info file
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

Utilities

get_package_info()
Package info utility
get_session_info()
Session info utility