search

Zafar-Lab / Margaret

Metric learning-based graph-partitioned trajectory inference from single-cell data
MIT License
11 stars 5 forks source link

Where to get prior information of Starting cell for Margaret? #38

Closed Rohit-Satyam closed 1 year ago

Rohit-Satyam commented 1 year ago

I observed that Margaret uses Palantir_pseudotime information and requires user to have prior knowledge of starting cell. Is there an inbuilt function to identify which cells could be used as starting cells or we have to run some other tools to find that out? I think choosing any cell arbitrarily as starting point will be wrong!!

kpandey008 commented 1 year ago

The starting cell needs to be specified as an input for Margaret. It is possible to identify the starting cells usually using some exploratory analysis like clustering (and then projecting expressions of known marker genes in start cells on the 2d-embedding visualization) or from prior biological knowledge about the dataset you are working with. Choosing an arbitrary starting cell will likely result in incorrect pseudotime and trajectory analysis