Single cell RNA-seq

We offer end-to-end processing of data from 10x Genomics Chromium gene expression assays and other single-cell RNA-seq platforms. Raw reads are mapped to the reference genome using Cell Ranger (10x Genomics) or other appropriate alignment tools, generating per-sample count matrices. Downstream analyses are performed with Seurat and complementary R packages, covering quality control, normalization, dimensionality reduction, clustering, differential gene expression, cell-type annotation, and visualization. Single-cell VDJ (immune repertoire) analysis is also supported. Please contact us if you are unsure whether your technology is supported.

 

  • Optional: Run summary metrics and quality charts in HTML format (optional)
  • HTML reports covering quality control, filtering, and normalization
  • HTML reports for integration, clustering, differential gene expression, gene ontology and pathway enrichment analysis, and automatic cell-type annotation
  • Interactive Shiny app for exploring your results
  • Filtered and/or unfiltered feature-barcode matrices in MEX format (optional)
  • Read alignment files in BAM format with index (optional)
  • Loupe Cell Browser file for visualization and exploration (optional)
  • Intermediate results for custom downstream analysis (optional)

 

For more extensive analyses — such as trajectory analysis — we also offer project-based collaborations. Please contact us at projects@bioinformatics.unibe.ch for more details.

Example reports from a representative analysis are available for download below.

 

Note that we also offer more extensive downstream analyses (e.g. trajectory analysis) in the form of collaborations. Please contact us for more details.
HTML reports from an example analysis can be downloaded below.