Spatial Transcriptomics Analysis
We provide comprehensive preprocessing and analysis of 10x Genomics Visium spatial gene expression data. Our pipeline begins with spaceranger count, which performs fiducial detection, aligns reads to the reference genome, and generates count matrices. We then conduct extensive downstream analysis using Seurat and complementary R packages to deliver publication-ready results including quality control, normalization, clustering, differential gene expression, automated cell-type annotation, spatial variable gene identification, neighborhood analysis, cell-type deconvolution, and customized visualizations.
What You'll Receive:
Reports & Analysis:
- HTML quality control and preprocessing report
- Integration and clustering reports with publication-quality figures
- Differential gene expression analysis with functional enrichment analysis (gene ontology and pathway analysis)
- Automated cell-type annotation report
- Spatial variable gene identification report
- Cell-type deconvolution results
- Interactive Shiny app for exploring and visualizing your results
Data Outputs (optional):
Beyond Standard Analyses:
We also offer customized collaborative analyses tailored to your specific research questions. Please contact us at projects@bioinformatics.unibe.ch for more details.
Example Reports:
Interactive ShinyApp (Username: user1, password: weiKi0oh)
