_pkgdown.yml

destination: docs

template:
  params:
    part_of: evoverse
    footer: G. Caravagna, PhD.
url:
  caravagnalab.github.io/CNAqc

repo:
  url:
    home: https://github.com/caravagnalab/CNAqc/
    source: https://github.com/caravagnalab/CNAqc
    issue: https://github.com/caravagnalab/CNAqc/issues
    user: https://github.com/caravagnalab


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

reference:
- title: Available data
  desc:  References and datasets included in the package.
  contents:
  - chr_coordinates_hg19
  - chr_coordinates_GRCh38
  - gene_coordinates_GRCh38
  - DriverDBv3
  - example_dataset_CNAqc
  - example_PCAWG
  - fpr_test

- title: Data processing
  desc:  Functions to manipulate and visualise the data.
  contents:
  - annotate_variants
  - init
  - Mutations
  - CNA
  - inspect_segment
  - get_drivers
  - plot_segment_size_distribution
  - plot_karyotypes
  - plot_data_histogram
  - plot_gw_counts
  - plot_gw_depth
  - plot_gw_vaf
  - plot_segments
  - plot_multisample_CNA
  - plot_icon_CNA
  - split_by_chromosome
  - subsample
  - subset_by_segment_karyotype
  - subset_by_segment_totalcn
  - subset_by_minimum_CCF
  - subset_snvs
  - print.cnaqc
  - plot.cnaqc


- title: Purity and ploidy QC
  desc:  Analysis of CNA calls by peak detection.
  contents:
  - analyze_peaks
  - auto_tolerance
  - plot_peaks_analysis
  - plot_qc

- title: CCF estimation
  desc:  Computation of Cancer Cell Fractions data.
  contents:
  - compute_CCF
  - CCF
  - plot_CCF
  - plot_gw_ccf


- title: Smoothing
  desc:  Analysis and plotting functions to smooth segments.
  contents:
  - smooth_segments
  - plot_smoothing

- title: Overfragmentation detection
  desc:  Analysis and plotting functions to smooth segments.
  contents:
  - detect_arm_overfragmentation
  - plot_arm_fragmentation

- title: Pipelines
  desc:  Pipelines implemented with CNAqc.
  contents:
  - Sequenza_CNAqc
  - parse_Battenberg