search

Katsevich-Lab / sceptre

An R package for single-cell CRISPR screen data analysis emphasizing statistical rigor, massive scalability, and ease of use.
https://katsevich-lab.github.io/sceptre/
GNU General Public License v3.0
24 stars 7 forks source link

The difference between sceptre or seurat Mixscape? #139

Closed xiasijian closed 3 weeks ago

xiasijian commented 1 month ago

I am sorry that I am a beginner for perturb-seq, I want to know how I can use the result of sceptre for the input of seurat? Can the sceptre do clustering?

xiasijian commented 1 month ago

@ekatsevi

timothy-barry commented 4 weeks ago

Hi. No, sceptre and Seurat do not interoperate. sceptre does not currently do clustering. Its focus is on gRNA assignment and gRNA-to-gene association testing. The goal of Seurat mixscape is to remove ineffective perturbations (or cells that "escaped" perturbation). sceptre does not currently have functionality for removing ineffective perturbations, but we hope to add such functionality in the near future. In summary sceptre and Seurat can be thought of as complementary packages.

xiasijian commented 4 weeks ago

Hi. No, sceptre and Seurat do not interoperate. sceptre does not currently do clustering. Its focus is on gRNA assignment and gRNA-to-gene association testing. The goal of Seurat mixscape is to remove ineffective perturbations (or cells that "escaped" perturbation). sceptre does not currently have functionality for removing ineffective perturbations, but we hope to add such functionality in the near future. In summary sceptre and Seurat can be thought of as complementary packages.

Thanks a lot. Your interpretation is so distinct.