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zhanghao-njmu / SCP

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
https://zhanghao-njmu.github.io/SCP/
GNU General Public License v3.0
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Question about several functions in SCP #227

Open Cathearty opened 9 months ago

Cathearty commented 9 months ago

it is a very dramatic and fantastic package that almost rebuilds the whole knowledge system of beginners! However, there are a few questions I feel uncertain about and want to discuss with the author and colleagues.

  1. Does SCP support cellchat or similar cell-cell communication functions? I'd like to make a whole workflow built by SCP, but I failed to find which function may be suitable for this function.
  2. Does SCP support further analysis based on pseudotime analysis? In many cases, I want to perform further exploration after simply pseudotime analysis, but I failed to find the functions that support analysis such as how gene expression changes with the pseudo-time progress. I know this function is supported by Monocle3 (if it is supported in SlingShot I am not certain) and I can see how genes change from the early stage of differentiation to the terminals.

That's all my questions and it will be greatly helpful if there are replies!

MInsYang commented 5 months ago

Hello, I am not an SCP developer, but based on my experience using it, I would say 1. no. 2. you may refer to the parameters of RunDynamicFeature for more information.