dbSequence/_pkgdown.yml at dev · dbverse-org/dbSequence · GitHub

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url: https://github.com/dbverse-org/dbsequence-r
template:
  bootstrap: 5

reference:
- title: Data Import
  desc: high-level import functions
  contents:
  - read_bed
  - read_vcf
  - read_bam
  - read_gff
  - read_gff3

- title: Range Operations (plyranges-like)
  desc: Functions for manipulating genomic ranges
  contents:
  - filter_by_overlaps
  - compute_coverage
  - as_granges
  - asRanges
  - as_ranges-dbSequence-method

- title: BiocIO Import Interface
  desc: BiocIO-compatible import methods for genomic data files
  contents:
  - DuckDBFile-class
  - DuckDBFile
  - import,BamFile,missing,ANY-method
  - import,BEDFile,missing,ANY-method
  - import,VcfFile,missing,ANY-method
  - import,GFFFile,missing,ANY-method
  - import,GTFFile,missing,ANY-method
  - import,character,missing,ANY-method
  - import,FastaFile,missing,ANY-method
  - show,DuckDBFile-method

- title: Object Classes
  desc: S4 classes and constructors
  contents:
  - dbSequence-class
  - dbSequence
  - show,dbSequence-method

- title: Accessors
  desc: Accessor functions for dbSequence objects
  contents:
  - tableName
  - fileSource
  - table_name
  - file_source
  - fileSource<-

- title: Conversion
  desc: Conversion between dbSequence and other formats
  contents:
  - coerce,dbSequence,GRanges-method
  - coerce,GRanges,dbSequence-method

- title: Internal Functions
  desc: Internal package functions
  contents:
  - starts_with(".")

articles:
- title: Articles
  navbar: ~
  contents:
  - data-ingestion
  - plyranges-api

navbar:
  structure:
    left: [intro, reference, articles]
    right: [search, github]
  components:
    articles:
      text: Articles
      menu:
      - text: Data Ingestion
        href: articles/data-ingestion.html
      - text: plyranges API
        href: articles/plyranges-api.html