_pkgdown.yml

url: https://github.com/cmatKhan/llfsRnaseq

template:
  params:
    bootswatch: cosmo

navbar:
  structure:
    left:  [intro, articles, reference, news, Citations, rnaseq_pipeline, rnavar_pipeline, llfs]
    right: [search, github]
  components:
    articles:
      text: Vignettes
      menu:
      - text: The RNAseq Database
      - text: Overview
        href: articles/database-overview.html
      - text: -------------------------------
      - text: Processing Raw Data
      - text: Running the nf-core/rnaseq pipeline
        href: articles/create-samplesheet.html
      - text: Running the modified nf-core/rnavar pipeline
        href: articles/rna-dna-variant-compare.html
      - text: --------------------------------
      - text: Initial QC
      - text: Sex Label Check
        href: articles/sex-label-check.html
      - text: Expression QC
        href: articles/expression-qc.html
      - text: Batch Effects
        href: articles/batch-effects.html
      - text: --------------------------------
      - text: Creating a release
      - text: Setting filters and Exporting the Data
        href: articles/creating-a-release.html
    reference:
      text: API
      href: reference/index.html
    rnaseq_pipeline:
      text: nf-core/rnaseq pipeline
      href: https://nf-co.re/rnaseq/3.3/
    rnavar_pipeline:
      text: modified nf-core/rnavar
      href: https://github.com/cmatKhan/rnavar
    llfs:
      test: LLFS
      href: https://longlifefamilystudy.wustl.edu
    github:
      icon: fa-github fa-lg
      href: https://github.com/cmatKhan/llfsRnaseq

reference:
- title: Handling Raw Data
  desc: These functions assist with running the nf-core/rnaseq pipeline
    and handling the output
  contents:
  - combine_txi_objects
- title: Sex Mislabe QC Functions
  desc: These functions are used in the Sex Mislabelling QC Vignette
  contents:
  - sex_mislabel_setup
  - top_500_pca_for_sex_mislabels
- title: Batch Effect QC Functions
  desc: These functions are used in in the Batch Effects QC Vignette
  contents:
  - batch_effect_qc_setup
  - before_after_pca_and_plate_regression_plots
  - direction_change_in_percent_intergenic
  - filter_dds_restimate_sizeFactors
  - project_counts_onto_orig_pcs
  - remove_parameter_effects
- title: Variant Comparison
  desc: Functions used to compare RNA variant and WGS data
  contents:
  - parse_all_by_all_compiled_results

home:
  links:
  - text: Ask a question
    href: https://github.com/cmatKhan/llfsRnaseq/discussions
  - text: Request a feature
    href: https://github.com/cmatKhan/llfsRnaseq/issues