Contributions by Tianyang Xu, Pei Lin, Riccardo Calandrelli, Ekko Zhu, Chi Zhang, Qiuyang Wu in the Sheng Zhong Lab.
HiFi-Slide is a super-resolution spatial transcriptomics sequencing technology. This technique captures and spatially resolves genome-wide RNA expression in a submicron resolution for fresh-frozen tissue.
All published computational tools used for HiFi-Slide data analysis are free software. We installed all of them under one conda environment.
Required software:
- PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593
- Rozowsky, J., Kitchen, R. R., Park, J. J., Galeev, T. R., Diao, J., Warrell, J., Thistlethwaite, W., Subramanian, S. L., Milosavljevic, A., & Gerstein, M. (2019). exceRpt: A Comprehensive Analytic Platform for Extracellular RNA Profiling. Cell systems, 8(4), 352–357.e3. https://doi.org/10.1016/j.cels.2019.03.004
- Documentation of the latest developed scripts that can be run from the command line using input parameters.