_pkgdown.yml

template:
  params:
    bootswatch: cosmo
reference:
- title: Splicejam core functions
  desc: These functions are the heart of the splicejam package
  contents:
  - has_concept("splicejam core functions")
- title: RNA-seq functions
  desc: Functions aimed at RNA-seq analysis
  contents:
  - has_concept("jam RNA-seq functions")
- title: Splicejam R-shiny functions
  desc: Functions to enable Splicejam R-shiny
  contents:
  - has_concept("splicejam R-shiny functions")
- title: ALE-specific RNA-seq functions
  desc: Functions specific to ALE (alternate last exon) RNA-seq analysis
  contents:
  - has_concept("jam ALE-specific RNA-seq functions")
- title: RNA-seq codon usage functions
  desc: Functions specific to codon usage in RNA-seq analysis
  contents:
  - has_concept("jam codon usage functions")
- title: GRanges functions
  desc: Functions to manipulate the Genomic Ranges (GRanges) family of objects
  contents:
  - has_concept("jam GRanges functions")
- title: Design functions
  desc: Functions aimed at manipulation of experimental design
  contents:
  - has_concept("jam design functions")
- title: Plot functions
  desc: Functions that assist with R plotting
  contents:
  - has_concept("jam plot functions")
- title: ggplot2 functions
  desc: Functions specific to ggplot2 visualization
  contents:
  - has_concept("jam ggplot2 functions")
- title: List functions
  desc: Functions that assist with list manipulation
  contents:
  - has_concept("jam list functions")
- title: String functions
  desc: Functions aimed at manipulation of character strings
  contents:
  - has_concept("jam string functions")
- title: Spatial functions
  desc: Functions that assist with spatial data, particularly 3-D coordinates
  contents:
  - has_concept("jam spatial functions")
- title: Color functions
  desc: Functions that assist with color manipulation
  contents:
  - has_concept("jam color functions")
- title: Matrix functions
  desc: Functions aimed at manipulation of matrix data
  contents:
  - has_concept("jam matrix functions")
- title: Numeric functions
  desc: Functions aimed at manipulation of numeric data
  contents:
  - has_concept("jam numeric functions")
- title: splicejam test data
  desc: R data with exons, coverage, and splice junctions
  contents:
  - has_concept("splicejam data")
- title: Import functions
  desc: Functions to import specific data formats
  contents:
  - has_concept("jam data import functions")