Updates to Navbar

README.md

@@ -4,7 +4,7 @@
 
 The Single Cell Toolkit (SCTK) in the *singleCellTK* R package is an analysis platform that provides an **R interface to several popular single-cell RNA-sequencing (scRNAseq) data preprocessing, quality control, analysis, and visualization tools**. SCTK imports raw or filtered counts from various scRNAseq preprocessing tools such as 10x CellRanger, BUStools, Optimus, STARSolo, and more. By integrating several publicly available tools written in R or Python, SCTK can be used to perform extensive quality control including doublet detection, ambient RNA removal. SCTK integrates analysis workflows from popular tools such as Seurat and Bioconductor/OSCA into a single unified framework. Results from various workflows can be summarized and easily shared using comprehensive HTML reports. Lastly, data can be exported to Seurat or AnnData object to allow for seamless integration with other downstream analysis workflows.
 
-![](https://camplab.net/sctk/img/interior-2.png)
+![](https://camplab.net/sctk/SingleCellTK_summary.png)
 
 ## Features
 

_pkgdown.yml

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       href: articles/installation.html
     - text: "Tutorials"
       menu:
-      - text: "Importing and QC - PBMC3K"
-        href: articles/01_import_and_qc_tutorial.html
-      - text: "A La Carte Workflow - PBMC3K"
-        href: articles/02_a_la_carte_workflow.html
-      - text: "Seurat Curated Workflow - PBMC3K"
-        href: articles/seurat_curated_workflow.html
-      - text: "Celda Curated Workflow - PBMC3K"
-        href: articles/celda_curated_workflow.html
-      - text: "Scanpy Curated Workflow - PBMC3K"
-        href: articles/scanpy_curated_workflow.html
+         - text: "Basic workflows"
+           menu:
+            - text: "PBMC3K"
+              href: articles/01_import_and_qc_tutorial.html
+         - text: ---------------------
+         - text: "Detailed Documentation"
+           menu:
+              - text: "Data"
+                menu:
+                  - text: "Import Data"
+                    href: articles/import_data.html
+                  - text: "Import Gene Sets"
+                    href: articles/import_genesets.html
+                  - text: "Annotation"
+                    href: articles/import_annotation.html
+                  - text: "Export Data"
+                    href: articles/export_data.html
+                  - text: "Delete Data"
+                    href: articles/delete_data.html
+              - text: "QC & Filtering"
+                menu:
+                  - text: "Droplet QC (R console)"
+                    href: articles/cnsl_dropletqc.html
+                  - text: "Cell QC (R console)"
+                    href: articles/cnsl_cellqc.html
+                  - text: "Cell QC (Shiny UI)"
+                    href: articles/ui_qc.html
+                  - text: "Filtering"
+                    href: articles/filtering.html
+              - text: "Normalization & Batch Correction"
+                menu:
+                  - text: "Normalization"
+                    href: articles/normalization.html
+                  - text: "Batch Correction"
+                    href: articles/batch_correction.html
+              - text: "Feature Selection & Dimensionality Reduction"
+                menu:
+                 - text: "Feature Selection"
+                   href: articles/feature_selection.html
+                 - text: "Dimensionality Reduction"
+                   href: articles/dimensionality_reduction.html
+                 - text: "2D Embedding"
+                   href: articles/2d_embedding.html
+              - text: "Clustering"
+                menu:
+                   - text: "Basic clustering"
+                     href: articles/clustering.html
+                   - text: "Seurat Curated Workflow - PBMC3K"
+                     href: articles/seurat_curated_workflow.html
+                   - text: "Celda Curated Workflow - PBMC3K"
+                     href: articles/celda_curated_workflow.html
+                   - text: "Scanpy Curated Workflow - PBMC3K"
+                     href: articles/scanpy_curated_workflow.html
+              - text: "Differential Expression & Cell Type Labeling"
+                menu:
+                - text: "Differential Expression"
+                  href: articles/differential_expression.html
+                - text: "Find Marker"
+                  href: articles/find_marker.html
+                - text: "Cell Type Labeling"
+                  href: articles/cell_type_labeling.html
+              - text: "Pathway & Enrichment Analysis"
+                menu:
+                - text: "EnrichR"
+                  href: articles/enrichR.html
+                - text: "Pathway Analysis"
+                  href: articles/pathwayAnalysis.html
+              - text: "Trajectory Analysis"
+                menu:
+                - text: "TSCAN"
+                  href: articles/trajectoryAnalysis.html
+              - text: "Visualization"
+                menu:
+                - text: "General Visualization"
+                  href: articles/visualization.html
+                - text: "Generic Heatmap"
+                  href: articles/heatmap.html
+              - text: "Web Application"
+                menu:
+                 - text: "FAQs"
+                   href: articles/webApp.html
     - text: "SCTK-QC"
       href: articles/cmd_qc.html
-    - text: "Documentation"
-      menu:
-        - text: "Data"
-          menu:
-            - text: "Import Data"
-              href: articles/import_data.html
-            - text: "Import Gene Sets"
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-            - text: "Annotation"
-              href: articles/import_annotation.html
-            - text: "Export Data"
-              href: articles/export_data.html
-            - text: "Delete Data"
-              href: articles/delete_data.html
-        - text: "QC & Filtering"
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-            - text: "Droplet QC (R console)"
-              href: articles/cnsl_dropletqc.html
-            - text: "Cell QC (R console)"
-              href: articles/cnsl_cellqc.html
-            - text: "Cell QC (Shiny UI)"
-              href: articles/ui_qc.html
-            - text: "Filtering"
-              href: articles/filtering.html
-        - text: "Normalization & Batch Correction"
-          menu:
-          - text: "Normalization"
-            href: articles/normalization.html
-          - text: "Batch Correction"
-            href: articles/batch_correction.html
-        - text: "Feature Selection & Dimensionality Reduction"
-          menu:
-          - text: "Feature Selection"
-            href: articles/feature_selection.html
-          - text: "Dimensionality Reduction"
-            href: articles/dimensionality_reduction.html
-          - text: "2D Embedding"
-            href: articles/2d_embedding.html
-        - text: "Clustering"
-          href: articles/clustering.html
-        - text: "Differential Expression & Cell Type Labeling"
-          menu:
-            - text: "Differential Expression"
-              href: articles/differential_expression.html
-            - text: "Find Marker"
-              href: articles/find_marker.html
-            - text: "Cell Type Labeling"
-              href: articles/cell_type_labeling.html
-        - text: "Pathway & Enrichment Analysis"
-          menu:
-            - text: "EnrichR"
-              href: articles/enrichR.html
-            - text: "Pathway Analysis"
-              href: articles/pathwayAnalysis.html
-        - text: "Trajectory Analysis"
-          menu:
-            - text: "TSCAN"
-              href: articles/trajectoryAnalysis.html
-        - text: "Curated Workflows"
-          menu:
-            - text: "Seurat"
-              href: articles/seurat_curated_workflow.html
-            - text: "Celda"
-              href: articles/celda_curated_workflow.html
-        - text: "Visualization"
-          menu:
-          - text: "General Visualization"
-            href: articles/visualization.html
-          - text: "Generic Heatmap"
-            href: articles/heatmap.html
-        - text: "Web Application"
-          menu:
-          - text: "FAQs"
-            href: articles/webApp.html
+
     - text: "Reference"
       href: reference/index.html
     - text: "NEWS"