BASiCS spike info for single cell RNA sequences or Bayesian statistics help
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@alexandriapinto1-13151
Last seen 3.7 years ago

Hi, 

I am dealing with a dataset and I do not believe any spike in were included. I want to use BASiCS to help my clustering but it requires the use of spike information. Is there a way to use BASiCs without the information?

Alternatively, is there another package I could use to use bayesian statistics on my data? 

 

 

BASiCS bayesian single cell scrnaseq • 560 views
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CataVallejos ▴ 10
@catavallejos-13762
Last seen 2.1 years ago
MRC Human Genetics Unit & The Alan Turi…

Hello,

Indeed, the current release of BASiCS (BioC 3.6) cannot be used without spike-ins. Recently, we extended the method to the no-spikes case and that is available in BioC devel (see also https://www.biorxiv.org/content/early/2017/12/21/237214)

 

However, I am afraid that BASiCS is *not* suitable for clustering analyses. This is because BASiCS has been designed in the context of supervised experimental designs only (e.g. case/control). Applying BASiCS in a clustering context is not advised and therefore I would refer you to other libraries that are specifically designed for clustering (e.g. SC3). 

My apologies for not being more helpful this time.

Best

Cata

 

 

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Ah okay! Thank you anyway

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