_pkgdown.yml

url: https://oist.github.io/GenomicBreaks
template:
  bootstrap: 5
reference:
  - title: Plotting functions
    desc: Graphical display of pairwise alignments
  - contents:
    - has_concept("plot functions")
  - title: Heatmap Functions
    desc: Functions that return a `Heatmap` object from the `heatmaps` package.
  - contents:
    - has_concept("heatmap functions")
  - title: genoPlotR functions
    desc: Functions related to the `genoPlotR` package that we use for pair chromosome plots.
  - contents:
    - has_concept("genoPlotR functions")
  - title: Distance functions
    desc: Various ways to estimate the similarity between two genomes.
  - contents:
    - has_concept("Similarity indexes")
  - title: Colinearity functions
    desc: Functions to analyse colinearity and synteny.
  - contents:
    - has_concept("Colinearity functions")
  - title: Flags and filters
    desc: Functions to flag patterns of alignments and filter them.
  - contents:
    - starts_with("flag")
    - starts_with("filter")
    - starts_with("show")
  - title: Bioconductor API functions
    desc: Functions that provide compatibility with GRanges, etc.
  - contents:
    - has_concept("Bioconductor API functions")
  - title: Motifier functions
    desc: Functions that take `GBreaks` objects and return them modified.
  - contents:
    - has_concept("modifier functions")
  - title: Reducing functions
    desc: Functions that take `GBreaks` objects and return simpler `GRanges` objects.
  - contents:
    - has_concept("Reducing functions")
  - title: Converter functions
  - contents:
    - has_concept("Converter functions")
  - title: Scaffolding functions
    desc: Functions to aid trivial scaffolding
  - contents:
    - has_concept("scaffolding functions")
  - title: Other functions
  - contents:
    - StructuralVariants
    - align_scaf_plot_2
    - bp_coverage
    - feature_coverage
    - int_frag
    - inv2UCSCData
    - isSorted
    - leftInversionGaps
    - load_genomic_breaks
    - makeInversion.chr
    - orderQuerySeqLevels
    - readMAF
    - scaf_align_plot
    - tan_bp
    - zipWithNext