_pkgdown.yml

url: https://katsevich-lab.github.io/sceptre/
template:
  assets: .r_examples/r_examples
  bootstrap: 5

home:
  links:
    - text: Report a bug
      href: https://github.com/Katsevich-Lab/sceptre/issues
  sidebar:
    structure: [links, license, citation, authors, custom, dev]
    components:
      custom:
        title: Funders
        text: |
          [Analytics at Wharton](https://analytics.wharton.upenn.edu/)

          [National Science Foundation](https://www.nsf.gov/)

reference:
- title: "Package documentation"
  contents:
  - sceptre

- title: "Pipeline functions"
  desc: >
    The functions that form the basis of the `sceptre` pipeline
  contents:
  - import_data
  - import_data_from_cellranger
  - import_data_from_parse
  - set_analysis_parameters
  - assign_grnas
  - run_qc
  - run_calibration_check
  - run_power_check
  - run_discovery_analysis

- title: "Plotting functions"
  desc: >
    Functions to visualize the analysis
  contents:
  - plot,sceptre_object-method
  - plot_grna_count_distributions
  - plot_assign_grnas
  - plot_run_qc
  - plot_run_calibration_check
  - plot_run_discovery_analysis
  - plot_run_power_check
  - plot_covariates

- title: "Pair constructor functions"
  desc: >
    Functions to facilitate the construction of discovery pairs and positive control pairs
  contents:
  - construct_positive_control_pairs
  - construct_cis_pairs
  - construct_trans_pairs

- title: "Information extraction functions"
  desc: >
    Functions to extract information and results from a `sceptre_object`
  contents:
  - print,sceptre_object-method
  - write_outputs_to_directory
  - get_result

- title: "Data"
  desc: >
    Example data to illustrate use of the functions
  contents:
  - highmoi_example_data
  - grna_target_data_frame_highmoi
  - lowmoi_example_data
  - gene_position_data_frame_grch38

authors:
  sidebar:
    roles: [aut, ctb, ths]

navbar:
  left:
  - icon: fa-play
    text: Get started
    href: articles/sceptre.html
  - icon: fa-book
    text: Manual
    href: https://timothy-barry.github.io/sceptre-book/
  - icon: fa-question-circle-o
    text: FAQ
    href: https://timothy-barry.github.io/sceptre-book/faq.html
  - icon: fa-code
    text: Functions
    href: reference/index.html
  - icon: fa-history
    text: Changelog
    href: news/index.html
  - icon: fa-users
    text: Community
    href: https://github.com/Katsevich-Lab/sceptre/discussions