Spatial transcriptomics

We offer pre-processing of data from 10x Genomics Visium spatial gene expression assays. We use spaceranger count to perform fiducial detection and map the reads to the reference genome and count the number of reads overlapping with each gene to produce a count matrix for each sample. After that, we perform a downstream analysis with the R package Seurat, resulting in quality control, transformation, dimensionality reduction and clustering.

 

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

Downloads

spatial_RNAseq_integration-dimRed-clustering.html
(ignore the error message and click the download buttom on the top right)
spatial_RNAseq_qc-filtering-normalization.html