_pkgdown.yml

destination: docs

template:
  params:
    part_of: evoverse
    footer: G. Caravagna, PhD.
url:
  caravagnalab.github.io/TINC
  
repo:
  url:
    home: https://github.com/caravagnalab/TINC/
    source: https://github.com/caravagnalab/TINC
    issue: https://github.com/caravagnalab/TINC/issues
    user: https://github.com/caravagnalab


authors:
  Giulio Caravagna:
    href: https://www.caravagnalab.org

reference:
- title: Available data
  desc:  Example fit data, and data sampler.
  contents:
  - fit_example
  - random_TIN

- title: Data processing
  desc:  Functions to pre-process the data, mainly parsers.
  contents:
  - load_TINC_input
  - load_VCF_Canvas
  - load_VCF_Canvas_Manta
  - load_VCF_Strelka
  - load_VCF_CNA_DRAGEN
  - load_VCF_smallVar_DRAGEN


- title: Data analysis
  desc:  Functions to analyse the data, and plot results.
  contents:
  - autofit
  - to_string
  - plot_simple_report
  - plot_full_page_report
  
- title: S3 functions
  desc:  Functions to print and plot a `tinc_obj`
  contents:
  - plot.tin_obj
  - print.tin_obj

- title: CHIP analysis
  desc:  Functions to check for the presence of clonal hematopoiesis in normal/tumour bams
  contents:
  - check_CHIP_variants