_quarto.yml

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website:
  title: "COTAN Datasets analysis"
  sidebar:
    background: "#D9E3E4"
    style: "docked"
    search: true
    collapse-level: 1
    contents:
      - href: index.qmd
        text: Home
      - section: "Datasets"
        contents: 
        
        - section: "Mouse Cortex Loo 2019"
          contents:
          - href: Mouse_Cortex_E14.5.qmd
            text: "Cleaning and cell clustering"
          - href: geneCoexAnalysisDataset1.qmd
            text: "Coexpression analaysis"
            
        - section: "Mouse Cortex Yuzwa 2017"
          contents: 
          - href: CorticalCells_GSM2861511_E135-analysis.qmd
            text: "E13.5 Cleaning and cell clustering"
          - href: geneCoexAnalysisE13.5Yuzwa.qmd
            text: "Correlation analysis for E13.5"
          - href: CorticalCells_GSM2861514_E175-analysis.qmd
            text: "E17.5 Cleaning and cell clustering"
          - href: geneCoexAnalysisE17.5Yuzwa.qmd
            text: "Correlation analysis for E17.5"
            
        - section: "Mouse Brain LaManno 2021"
          contents: 
          - href: ForebrainDorsal_E135-analysis.qmd
            text: "E13.5 Cleaning and cell clustering"
          - href: geneCoexAnalysisE13.5MouseBrain.qmd
            text: "Correlation analysis for E13.5"
          - href: ForebrainDorsal_E150-analysis.qmd
            text: "E15.0 Cleaning and cell clustering"
          - href: geneCoexAnalysisE15.0MouseBrain.qmd
            text: "Correlation analysis for E15.0"
          - href: ForebrainDorsal_E175-analysis.qmd
            text: "E17.5 Cleaning and cell clustering"
          - href: geneCoexAnalysisE17.5MouseBrain.qmd
            text: "Correlation analysis for E17.5"
          - href: ForebrainLaManno2021ClustersGDI.qmd
            text: "Original Clusters GDI evaluation"
            
        - section: "CD14+"
          contents: 
          - href: cd14_analysis.qmd
            text: "CD14+ Cleaning and cell clustering"
        
        - section: "PBMC form 10X site"
          contents:
          - href: PBMC1_filtering.qmd
            text: "Cleaning PBMC1"
          - href: PBMC2_filtering.qmd
            text: "Cleaning PBMC2"
          - href: PBMC3_filtering.qmd
            text: "Cleaning PBMC3"
          - href: PBMC4_filtering.qmd
            text: "Cleaning PBMC4"
          
            
      - section: "Coex score evaluation"
        contents: 
        - href: generalCoexAssess.qmd
        
      - section: "GDI sensitivity"
        contents: 
        - href: OriginalClustersDistanceEvaluation.qmd
          text: "Clusters Distance Evaluation"
        - href: FindUniformOrigCluster.qmd
          text: "Cluster Unifomity and GDI score"
        - href: GDI_Increment_From_Mixing.qmd
          text: "GDI Increment From Mixing"
          
      - section: "Cluster evaluation"
        contents: 
        
        - href: NonCT_clusters.qmd
          text: "Not UT cluster with LR"
        
        - href: Real_UT_clustersByCotan.qmd
          text: "Real UT clusters with LR"
        
        - href: cd14_clusterizations_comparisons.qmd
          text: "CD14+ clusterizations"
        
          
        - href: clustering_comparison.ipynb
          text: "PBMCs clustering comparison"
          
        - href: probability_score.qmd
          text: "PBMCs probability score"
        
          
      - section: "DEA evaluation"
        contents: 
        - href: DEA_Type1Er.qmd
          text: "Type I error"
        - href: geneExpressionAnalysisUniformClusters.qmd
          text: "Explorative analysis of gene expression"
        - href: FDR_analisys.qmd
          text: "FDR analysis - define DE genes"
        - section: "FDR and TPR - ROC curves"
          contents: 
          - href: FDR_analisysResults3_10.qmd
            text: "Results - thresholds true 3% 10%"
          - href: FDR_analisysResults5_20.qmd
            text: "Results - thresholds true 5% 20%"
          - href: FDR_analisysResults5.qmd
            text: "Results - thresholds true 5%"
          - href: FDR_analysisResultsLFC.qmd
            text: "Results - Log Fold Change"
      
      - section: "Additional code and scripts"
        contents: 
        - href: src/scanpyTypeIError.py
          text: "ScamPy Type I Error code"
        - href: src/scanpyFDR.py
          text: "ScamPy FDR code"
        - href: scanpy.ipynb
          text: "Example of scanpy clustering and DEA"
        - href: scvi-tools.ipynb
          text: "Example of ScVI clustering and DEA"
        
        


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