single cell RNA profiling analysis of imaging-based spatial transcriptomics data
Project description
News
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Update with comseg 0.0.8. Compatibility with SOPA : https://gustaveroussy.github.io/sopa/
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Update with comseg 0.0.7. Computation of the co-expression matrix is now faster.
Support
If you have any questions relative to the package or bug, please open an issue in this repository.
ComSeg framework
A detail documentation is available at https://comseg.readthedocs.io/
Single cell spatial RNA profiling
ComSeg is an algorithm for single cell spatial RNA profiling in image-based transcriptomic data.
It takes as input a csv with the spot coordinates and output an anndata object with the genes expression and coordinates of each cell.
Citation
A point cloud segmentation framework for image-based spatial transcriptomic, Defard et al bioRxiv 2023.12.01.569528; doi: https://doi.org/10.1101/2023.12.01.569528
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