This repository contains the code (mostly in form of notebooks) to reproduce the study published in
N. Müller-Bötticher, S. Tiesmeyer, R. Eils, N. Ishaque, Sainsc: A Computational Tool for Segmentation-Free Analysis of In Situ Capture Data. Small Methods (2024) https://doi.org/10.1002/smtd.202401123
All data used in this study is publicly available.
- StereoSeq datasets are available on STOmicsDB MOSTA
- Xenium datasets were downloaded from the 10x website
- NovaST datasets were downloaded from GEO
- Mouse brain scRNAseq data from the study Yao et al 2021 were downloaded from the NeMO Archive and from the study Yao et al 2023 from the Allen Brain Cell Atlas
- Simulations from Benjamin et al 2024 were downloaded from zenodo; https://doi.org/10.5281/zenodo.11050996, https://doi.org/10.5281/zenodo.10950538