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cnio-bu / beyondcell

Beyondcell is a computational methodology for identifying tumour cell subpopulations with distinct drug responses in single-cell RNA-seq and Spatial Transcriptomics data.
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questions of PSc and SSc #30

Closed QSong-github closed 1 year ago

QSong-github commented 2 years ago

I would like to know how you identify the drug perturbation (PSc) and the drug sensitivity (SSc)? I am a little confused about this, since your tool starts with these. Thanks!

SGMartin commented 1 year ago

Hi @QSong-github

Both collections of signatures are derived from linear models, the differences being the data sources:

  1. PSc: We mine the CLUE/LINCS drug perturbation collection. In this case, the signatures capture the transcriptomic differences between perturbed/unperturbed cells.
  2. SSc: These are mined from multiple pharmacogenomics assays such as CTRP or GDSC. Briefly, we collect genes whose expression changes according to a cancer cell line's susceptibility to a given compound.