Supplementary code and data to our study of the developing human meninges by Vinsland et al. (manuscript in preparation).
(https://www.biorxiv.org/content/10.1101/2025.07.08.663122v1)
Visualizations of the complete dataset, as well as cell type specific subsets ("Superclasses"), are browsable at CELLxGENE.
- BAM files will be available from the European Genome/Phenome Archive (https://ega-archive.org/) under accession number TBA.
- Complete count matrices (gene x cell counts) for the developing meninges and meningiomas are available as loom files here.
- The datasets can also be downloaded as .h5ad files from the browser: CELLxGENE.
- Raw Xenium data and images have been deposited at the BioImage Archive under accession number S-BIAD1600.
- Complete count matrices (gene x cell counts) for meningiomas are available as loom files here.
- Clustering was performed using the cytograph-dev version of cytograph. This is the version used for our adult human brain project. Its installation and usage are described here.
- Jupyter notebooks used to make figures are available here. The notebooks also import from cytograph-dev. (cytograph-shoji will not work).
- Jupyter notebooks used for Xenium data processing are found here.
- LDA models for topic modelling: model.bin cells.txt.