GRASP: Modeling Transcript Spot Graph Representations to Analyze Subcellular Patterns and Cell Clustering in High-Resolution Spatial Transcriptomics
Description
The simulated datasets were generated using the simFISH package, which can be accessed at sim-fish documentation (https://sim-fish.readthedocs.io/en/stable/). The cell line datasets (seqFISH+ fibroblast cells and MERFISH U2OS cells) that support the conclusions of this article are available in the Figshare repository at https://figshare.com/collections/Bento_Manuscript_Datasets/6564043/1. For the MERFISH mouse ileum dataset, data were obtained from https://doi.org/10.5061/dryad.jm63xsjb2. For the MERSCOPE mouse liver dataset, the data were sourced from the MERFISH Mouse Liver Map, available at https://info.vizgen.com/mouse-liver-data?submissionGuid=832a9f61-22d3-44c1-a2cf-838c166d9ac5. For the Xenium ST datasets of lung adenocarcinoma tissue, the data were acquired from v1 platforms, and both datasets were downloaded from the 10x Genomics dataset repository (https://www.10xgenomics.com/datasets/xenium-human-lung-cancer-post-xenium-technote).