Hi Alex. This is a great tool for non bioinformaticians. I'll be upskiling on this using R this year. Just did not know where to access the freely available spacial transcriptomics datasets . Thanks for this.
Of course! With so much data being public, there's so much rich data available that doesn't require researchers to run their own experiments and spend a ton of money. A large number of labs *only* use public data and do amazing work. We with our curiosity can do a lot with it! spatialGE makes it easier for researchers, and the website for everyone, to explore them. Hope for you to identify awesome findings. Also worth mentioning that if there's a study you'd like to explore (because each study can only spend so much time on analyses and there's so much that can be done), reaching out to corresponding authors often will get you data. For us as an example, our single cell data I'm sure the surgeon would be happy to share. Limitation is often the institution's legal team. Mine free data. Dream for many biologists and bioinformatians, alike. Also allows for validation of findings on independent samples. Sharing is the best thing in science because people think differently and have different hypotheses. Doesn't make sense to run the same experiment again if someone else has done so.
Hi Alex! Thank you for the fantastic resources - I'm a graduate student at UF and am currently working on a CosMx project. Any chance you are looking to collaborate? If so happy to provide my email.
Hey, Mack! Drive by UF every summer on my way from USF to MN - small world. Since I don't have my own lab nor covered time to do my "own" projects I wouldn't be able to have dedicated collaboration time that's salary covered. However, I'd be happy to provide some comments or feedback on things if you guys would need. Feel free to reach out via email on my page and can discuss.
