This repository is for practice in analyzing spatial transcriptomics data using Scanpy.
The workflow starts with the Space Ranger output file:
filtered_feature_bc_matrix.h5 (gene-by-spot count matrix).
- Kadur Lakshminarasimha Murthy, P., Sontake, V., Tata, A. et al.
Human distal lung maps and lineage hierarchies reveal a bipotent progenitor.
Nature 604, 111–119 (2022).
https://doi.org/10.1038/s41586-022-04541-3
-
Williams, C.G., Lee, H.J., Asatsuma, T. et al.
An introduction to spatial transcriptomics for biomedical research.
Genome Med 14, 68 (2022).
https://doi.org/10.1186/s13073-022-01075-1 -
Walker, B.L., Cang, Z., Ren, H. et al.
Deciphering tissue structure and function using spatial transcriptomics.
Commun Biol 5, 220 (2022).
https://doi.org/10.1038/s42003-022-03175-5
- Scanpy spatial transcriptomics tutorial:
https://scanpy-tutorials.readthedocs.io/en/multiomics/analysis-visualization-spatial.html