mkdocs.yml

site_name: scRNAbox
site_url: https://neurobioinfo.github.io/
nav:
    - Home: index.md
    - Pipeline:
        - 'Installation' : installation.md
        - 'Step 0: Set up' : Step0.md
        - 'Step 1: FASTQ to expression matrix' : Step1.md
        - 'Step 2: Seurat object and ambient RNA' : Step2.md
        - 'Step 3: Quality control and filtering' : Step3.md
        - 'Step 4: Doublet removal (standard)' : Step4.md
        - 'Step 4: Demultiplexing (HTO)' : Step4HTO.md
        - 'Step 5: Integration' : Step5.md
        - 'Step 6: Clustering' : Step6.md
        - 'Step 7: Cluster annotation' : Step7.md
        - 'Step 8: Differential gene expression' : Step8.md
    - Documentation:    
        - 'Job configurations' : config.md
        - 'Execution parameters' : reference.md 
        - 'Outputs': outputs.md 
        - 'Intepreting Log Files': Log.md 
    - Tutorial:
        - 'Downloading the Midbrain dataset' : midbrain_download.md
        - 'Standard analysis track: Midbrain dataset' : Dataset1.md
        - 'Analysis of DGE outputs' : DEG.md
        - 'Downloading the PBMC dataset' : pbmc_download.md
        - 'HTO analysis track: PBMC dataset' : Dataset2.md
        - 'Manual CellRanger library preparation' : library_prep.md     
    - About:
        - 'License': 'LICENSE.md'
        - 'Help and Feedback': contributing.md
        - 'Acknowledgement': Acknowledgement.md
theme: readthedocs