diff --git a/README.md b/README.md index 179124f36..abb4950b0 100644 --- a/README.md +++ b/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 diff --git a/SingleCellTK_summary.png b/SingleCellTK_summary.png new file mode 100644 index 000000000..98617e1b8 Binary files /dev/null and b/SingleCellTK_summary.png differ diff --git a/_pkgdown.yml b/_pkgdown.yml index 3866be872..041a91e68 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -221,92 +221,90 @@ navbar: 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" - 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" - 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" diff --git a/docs/404.html b/docs/404.html index 285f09d3f..adac98c96 100644 --- a/docs/404.html +++ b/docs/404.html @@ -55,163 +55,157 @@ - -
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