Spatial Transcriptomics Pipeline

The Spatial Transcriptomics pipeline is used to generate Spatial Transcriptomics datasets (containing gene counts for each spot) and basic statistics. As input, it uses the fastq files generated by the users sequencing platform. A manual description on how to use the pipeline is bundled within the pipeline itself.

The ST pipeline can be obtained from GitHub here.

For questions regarding the ST pipeline, please contact:
Jose Fernandez Navarro jose.fernandez.navarro@scilifelab.se