Chengyu, Li

Hi, @napaintian, thanks for your feedback. I have fixed this bug. You can install the latest version and try again.

Hi @napaintian, I've answered your question in https://github.com/ZJUFanLab/scRank/issues/1#issuecomment-2141336007. Could you please take a look there and let me know if you have any further questions?

Hi, thanks for your feedback. 1. The `rank` column is an intermediate variable that reflects the [sample ranks](https://rdrr.io/r/base/rank.html) of `perb_score` and can be ignored. The actual ranking of cell types...

Hi, @zqun1 Instead of running scRank separately for each dataset, I suggest treating each condition as a distinct cell state within the same cell type and running scRank on the...

Hi @zqun1, thanks for your feedback! We’ve added a `subsetScRank()` function for scRank objects, which allows you to subset the object based on metadata fields — similar to the subset()...

Hi, Luis Sorry for the delayed response. For your questions: 1. beyondcell (v2.2.0) We ran beyondcell following the tutorial’s default settings on each Seurat object (Melanoma, SCC47, JHU006). For example,...

Hi @luisherfurth , Thanks for raising this important point, it’s a valuable perspective. To clarify: When we designed the perturbation score in scRank, our primary goal was to rank cells...

Hi @luisherfurth, Below is a detailed breakdown of how to reproduce our results on the Kinker et al. dataset, 1. Preprocessing We followed a standard Seurat preprocessing pipeline with slight...

Hi @codedic. The error that occurs may be due to the default min_ModuleSize parameter in the ``init_mod`` function is set too small for your dataset, which causes the Dynamic cutree...

Hi @baiger1 , thanks for reporting this issue and for providing clear examples. I’ve checked the case and confirmed that the behavior is caused by a bug in `CreateScRank()`. The...