Analysis spatial transcriptomics data
Project description
StereoSiTE is a package for the analysis and visualization of spatial transcriptome data. It builds on top of anndata, scanpy and squidpy, from which it inherits modularity and scalability. It provides analysis tools to dissect cellular neighborhood based on cell composition and quantitatively define cell-cell communication in spatial.
StereoSiTE’s key applications
Cellular Neighborhood (CN) clustering based on cell composition of each bin
Spatial Cell Interaction Intensity (SCII) analysis
Citation
If you use stereosite in your work, please cite the publication as follows:
StereoSiTE: A framework to spatially and quantitatively profile the cellular neighborhood organized iTME
Xing Liu, Chi Qu, Chuandong Liu, Na Zhu, Huaqiang Huang, Fei Teng, Caili Huang, Bingying Luo, Xuanzhu Liu, Yisong Xu, Min Xie, Feng Xi, Mei Li, Liang Wu, Yuxiang Li, Ao Chen, Xun Xu, Sha Liao, Jiajun Zhang
bioRxiv 2022.12.31.522366; doi: https://doi.org/10.1101/2022.12.31.522366
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