Open hanhuajun40 opened 6 months ago
Hi Huajun,
Thank you for your feedback. And I apologize for the very late response.
For now, I can answer the second issue you raised. LUHMES CROP-seq analysis has a dedicated code repository. Functions you mentioned were located at: https://github.com/xinhe-lab/GSFA_paper/blob/master/R/plotting_functions.R. Please download the script and import those functions similar to:
source("../R/plotting_functions.R")
before running the tutorial.
Best, Lifan
Hi Huajun,
Somehow we missed the message you sent a long time ago. Sorry about this. Next time, you could also just email me directly (xinhe@uchicago.edu). About your questions, I'll answer 1) and 3):
1) You said you could't reproduce the results. What problems do you have? Does the program converge?
3) Our Supplementary Notes described how to select K, see Page 17: https://static-content.springer.com/esm/art%3A10.1038%2Fs41592-023-02017-4/MediaObjects/41592_2023_2017_MOESM1_ESM.pdf
Best, Xin
Hi, Xin,
I attempted to replicate the results from your GSFA tutorial using LUHMES CROP-seq data but encountered a few issues.
Thank you for providing such a powerful tool for perturbation analysis.
Best, Huajun