_quarto.yml

project:
  type: website
  execute-dir: project
  render:
    - analysis/index.qmd
    - analysis/Figure1_BulkTxomeAnalysis.qmd
    - analysis/Figure1_TableS1.qmd
    - code/Fig1_MetaCoverage.ipynb
    - analysis/Figure2_isoFraction.qmd
    - analysis/Figure2_novel_exons.qmd
    - analysis/Figure2_PlotGene.qmd
    - analysis/Figure2_plotNovelGenes.qmd
    - analysis/Figure2_NF1Locus.qmd
    - analysis/Figure2_PeptideSupport.qmd
    - analysis/Figure2_externalSupport.qmd
    - analysis/Figure3_IsoformSwitchAnalyzeR.qmd
    - analysis/Figure3_DTU_enrichments.qmd
    - analysis/Figure3_RBPEnrichments.qmd
    - analysis/Figure3_APA.qmd
    - analysis/Figure4_combinedNetworks.qmd
    - analysis/Figure4_Networks_Enrichments.qmd
    - analysis/Figure5_SeuratClustering.qmd
    - analysis/Figure5_MarkerGenesFigs.qmd
    - analysis/Figure5_TableS5D.qmd
    - analysis/Figure5_PseudotimeAnalysis.qmd
    - analysis/Figure5_Sankey.qmd
    - analysis/Figure6_rareVariant.qmd
    - analysis/Figure6_VEPConsequences.qmd
    - analysis/Figure6_TrackPlots.qmd
    - analysis/FigureS9_cor_plots.qmd
    - analysis/FigureS9_GH.qmd

website:
  title: "Dev Brain Iso-Seq"
  sidebar:
    style: "floating"
    tools:
      - icon: github
        href: https://github.com/gandallab/Dev_Brain_IsoSeq
    search: false
    contents:
      - analysis/Figure1_BulkTxomeAnalysis.qmd
      - analysis/Figure1_TableS1.qmd
      - code/Fig1_MetaCoverage.ipynb
      - text: "---"
      - analysis/Figure2_isoFraction.qmd
      - analysis/Figure2_plotNovelGenes.qmd
      - analysis/Figure2_PlotGene.qmd
      - analysis/Figure2_novel_exons.qmd
      - analysis/Figure2_NF1Locus.qmd
      - analysis/Figure2_PeptideSupport.qmd
      - analysis/Figure2_externalSupport.qmd
      - text: "---"
      - analysis/Figure3_IsoformSwitchAnalyzeR.qmd
      - analysis/Figure3_DTU_enrichments.qmd
      - analysis/Figure3_RBPEnrichments.qmd
      - analysis/Figure3_APA.qmd
      - text: "---"
      - analysis/Figure4_combinedNetworks.qmd
      - analysis/Figure4_Networks_Enrichments.qmd
      - text: "---"
      - analysis/Figure5_SeuratClustering.qmd
      - analysis/Figure5_MarkerGenesFigs.qmd
      - analysis/Figure5_TableS5D.qmd
      - analysis/Figure5_PseudotimeAnalysis.qmd
      - analysis/Figure5_Sankey.qmd
      - text: "---"
      - analysis/Figure6_rareVariant.qmd
      - analysis/Figure6_VEPConsequences.qmd
      - analysis/Figure6_TrackPlots.qmd
      - text: "---"
      - analysis/FigureS9_cor_plots.qmd
      - analysis/FigureS9_GH.qmd

format:
  html:
    theme: cosmo
    css: styles.css
    toc: true

execute:
  cache: true