scTAMsExplorer v1.0

Single-cell RNA-seq analysis - Interactive dashboard

Bioinformatics - scRNA-seq - Single-cell Atlas

Welcome to scTAMsExplorer

An interactive dashboard for exploring a single-cell RNA-seq atlas of human monocytes and macrophages profiled in vivo. All computations run live on the Seurat object passed to launch_explorer() .

How to use: Select any tab above. Set parameters in the left sidebar and press the action button. All results can be downloaded as PNG or CSV.

About this dataset

This atlas was generated by the Stanislas Goriely Laboratory from fetal hCD34+ MISTRG humanized mice, in which a human immune system develops from engrafted hematopoietic stem cells, allowing human monocyte-to-macrophage differentiation to be studied directly inside living tissue. It comprises single-cell transcriptomic profiles of monocytes and macrophages collected across multiple organs and tissue compartments, spanning both healthy sites and tumors (cell line-derived xenografts), to capture how macrophage states are shaped by their microenvironment. Cells were sequenced using 10x Genomics Chromium technology, aligned with Cell Ranger, and processed in Seurat with Harmony-based batch correction for cross-sample integration.

Dimensionality reduction: PCA + UMAP on the Harmony-corrected embedding ( umap.harmony ). Cell-type annotation at multiple resolution levels (Population_level1-3). Co-expression modules, Gene Regulatory Networks (GRNs) and TF activity inferred with hdWGCNA .

This atlas accompanies the preprint Regulatory Networks Shaping Human Tumor-Associated Macrophages In Vivo Identify MAFB as a Key Transcriptional Driver (Detavernier A., Donckier de Donceel E., Patanè F., et al., Research Square, 2026; doi:10.21203/rs.3.rs-8562817/v1 ), under review at Nature Communications .

10x Genomics Chromium Harmony integration Multi-level annotation TF regulon analysis hdWGCNA modules EnrichR pathway analysis
🗺

UMAP + Expression + Markers

  • UMAP coloured by any metadata column (e.g. Module activity scores. Mod-1/5)
  • FeaturePlot, VlnPlot, DotPlot, DoHeatmap
  • Blend mode: co-expression of two genes
  • Split violin / feature plot by any metadata
  • Top marker genes per cluster (FindMarkers)
  • Adjustable display size, font and DPI
🌋

DEGs + Volcano + Enrichment

  • Subset cells by any metadata value
  • FindMarkers between any two groups
  • Interactive volcano with ggrepel labels
  • p-value and log2FC threshold sliders
  • Enrichment run separately via EnrichR
  • Full geneset tables, UP and DOWN CSVs
🔗

Co-expression Modules

  • hdWGCNA hub gene tables (ranked by kME)
  • Module size overview table
  • Gene to Module lookup by gene name
  • Per-module pathway enrichment (EnrichR)
  • Sortable, filterable, paginated tables
🌐

Gene Regulatory Networks

  • Interactive drag-and-zoom visNetwork graph
  • 5 layout algorithms to choose from
  • Filter by Gain threshold and top N targets
  • Targets of a TF, regulators of a gene, or custom set
  • Optional colouring by module of origin
  • TF-TF only mode; PNG and CSV download
🎯

TF Regulon Heatmap

  • Dot heatmap: TF expression vs regulon activity
  • Side-by-side positive and negative regulons
  • Filter by module membership or manual TF list
  • Per-TF EnrichR enrichment (pos & neg)
  • PNG heatmap and data CSV download
⚙

Universal plot controls

  • Per-plot pixel size sliders for display
  • Separate inch + DPI controls for download
  • Font / label size slider on every plot
  • All tables: sortable, filterable, paginated
  • All results: PNG and CSV download buttons
Required R packages
Seurat ggplot2 dplyr tidyr plotly DT enrichR patchwork ggrepel visNetwork scales stringr tibble hdWGCNA
Stanislas Goriely Lab
Institute of Medical Immunology (IMI) - Université Libre de Bruxelles (ULB)
Dataset and analysis pipeline developed by Stanislas Goriely Laboratory.
Stanislas Goriely Lab - ULB
UMAP
Expression plot
Marker genes
DEG results
Volcano plot
UP-regulated enrichment
Geneset table
DOWN-regulated enrichment
Geneset table
Module sizes
Gene to Module lookup

                    

                  

                

                

                  
Hub genes per module

                  

                

                

                  

                    
                  

                  

                  

                  

                

              

            

          

          

            

              

                
              

              

                

                  

                    TF Interaction Network
                    Blue diamond = TF | Grey dot = target | Red = center | Blue edge = inhibition | Red edge = activation
                    

                      Modules (when coloured by module): 
                      ● Module 1  
                      ● Module 2  
                      ● Module 3  
                      ● Module 4  
                      ● Module 5
                    

                  

                  

                

              

            

          

          

            

              

                
              

              

                

                  
Regulon dot heatmap

                  

                  

                  

                

                

                  
Regulon summary

                  

                

                

                  

                    

                      
Positive regulon enrichment

                      Genes positively correlated (Cor > 0)
                      

                      

                    

                  

                  

                    

                      
Negative regulon enrichment

                      Genes negatively correlated (Cor < 0)