The repository shows the procedure followed to generate the example dataset for the nfcore-spatialxe pipeline Xenium ranger example dataset for the nfcore-spatialxe pipeline
Example dataset was downloaded from 10x Genomics website Data : Fresh Frozen Mouse Brain - Tiny Subset
wget https://cf.10xgenomics.com/samples/xenium/1.0.2/Xenium_V1_FF_Mouse_Brain_Coronal_Subset_CTX_HP/Xenium_V1_FF_Mouse_Brain_Coronal_Subset_CTX_HP_outs.zipUnzip the dataset, once unzipped the data size amounts to approx. 18Gb
unzip Xenium_V1_FF_Mouse_Brain_Coronal_Subset_CTX_HP_outs.zipInstall the following pip packages to run the python utility script
pip install -r requirements.txtUsage
$ python3 subset_data.py <path-to-xenium-bundle> <path-to-output-files>Contact
Sameesh Kher - [email protected] / [email protected]
Florian Heyl - [email protected] / [email protected]