_site.yml

name: "Glia IHC"
title: "IHC and ML to Phenotype AD Glia"
description: |
  APOE Glia
theme: theme.css
favicon: images/favicon.ico
base_url: https://serranopozolab.org/glia-ihc
repository_url: https://github.com/serrano-pozo-lab/glia-ihc
output_dir: "docs"
navbar:
  search: false
  source_url: https://github.com/serrano-pozo-lab/glia-ihc
  right:
    - text: "Home"
      href: index.html
    - text: "ROI Annotation"
      menu:
        - text: "Reorder Channels"
          href: reorder-channels
        - text: "---"
        - text: "Astrocyte Channel Extraction"
          href: aldh1l1-extraction
        - text: "Microglia Channel Extraction"
          href: iba1-extraction
        - text: "Plaque Channel Extraction"
          href: abeta-extraction
        - text: "Tangle Channel Extraction"
          href: phf1-extraction
    - text: "ROI Segmentation"
      menu:
        - text: "Parse VIA ROIs"
          href: parse-rois
        - text: "ROI Segmentation"
          href: roi-segmentation
        - text: "Parse ROI Measurements"
          href: parse-measurements
    - text: "Unsupervised ML"
      menu:
        - text: "Spectral Clustering"
          href: spectral-clustering
        - text: "Dimensionality Reduction"
          href: dimensionality-reduction
        - text: "Data Visualization"
          href: data-visualization
    - text: "Supervised ML"
      menu:
        - text: "Partition by Condition"
          href: partition-condition
        - text: "Partition by State"
          href: partition-state
        - text: "---"
        - text: "GBM by Condition"
          href: gbm-condition
        - text: "GBM by State"
          href: gbm-state
        - text: "---"
        - text: "Astrocyte CNN"
          href: astrocyte-cnn
        - text: "Microglia CNN"
          href: microglia-cnn
        - text: "Plot ROC Curves"
          href: plot-roc-curves
        - text: "---"
        - text: "Performance Evaluation"
          href: performance-evaluation       
output: distill::distill_article