splicejam/_pkgdown.yml at master · jmw86069/splicejam · GitHub

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destination: docs
home:
  title: Analysis and Visualization of Gene Splice Variants and Transcriptome Data
  description: Splicejam sashimi plots created using 'BigWig' and junction 'BED' files.
figures:
  fig.width: 8
  fig.height: 8
template:
  bootstrap: 5
  bootswatch: cosmo
url: https://jmw86069.github.io/splicejam/
reference:
- title: Splicejam core functions
  desc: These functions are the heart of the splicejam package
  contents:
  - has_concept("Splicejam core functions")
- title: Detected transcripts
  desc: Method to define detected transcripts, and review results
  contents:
  - has_concept("Detected transcripts")
- title: Data import functions
  desc: Useful wrapper functions to import genomic data
  contents:
  - has_concept("Data import functions")
- title: Splicejam Test data
  desc: Various data objects to test Splicejam
  contents:
  - has_concept("Splicejam data")
- title: Plot utility functions
  desc: Several functions, including 3-D BGA plotly function
  contents:
  - has_concept("Plot utility functions")
- title: Design functions
  desc: Support for statistical design and differential isoform analysis
  contents:
  - has_concept("Design functions")
- title: GenomicRanges functions
  desc: GenomicRanges utilities, such as annotating one GR or GRL from another
  contents:
  - has_concept("GenomicRanges functions")
- title: GTF functions
  desc: Gene-exon structure (GTF) file parsing to tx2gene data.frame, and others.
  contents:
  - has_concept("GTF functions")
- title: ALE and codon functions
  desc: Functions supporting Farris et al, alternate last exon (ALE) and codon usage analysis.
  contents:
  - has_concept("ALE and codon functions")
- title: Shiny prep functions
  desc: Functions to prepare the Splicejam R-shiny app
  contents:
  - has_concept("Shiny prep functions")
- title: Sashimi prep functions
  desc: Functions to prepare the Sashimi data and plot objects
  contents:
  - has_concept("Sashimi prep functions")
- title: ggplot2 customizations
  desc: Customizations to ggplot2 objects for Sashimi visualizations
  contents:
  - has_concept("ggplot2 customizations")
- title: Internal utility functions
  desc: Numerous utility functions, mostly for internal use within Splicejam
  contents:
  - has_concept("Internal utility functions")