stable_genes.rds missing

[Martin-Fahrenberger]

Hi pipeComp Team,

I read your preprint with great interested and immediately wanted to replicate your scRNA-seq pipeline benchmark, and eventually add some additional methods I m interested in. However, in order to replicate the normalization comparison the norm.stableG function requires the list of stable genes. For this it simply tries to read "~/pipComp/stable_genes.rds" but as far as I can tell this object has not been provided on github or figshare. I gather that it was built from the table of stable genes provided in "Stably expressed genes in single-cell RNA sequencing" by Julie M. Deeke et al.

It would be great if you could share the stable_genes.rds or point me at where it is shared if I missed it.

Thank you in advance,

Martin Fahrenberger

[plger]

Hi,
thanks for pointing this out. You'll find the file here:
https://github.com/plger/pipeComp/blob/devel/data/stableG.RData
It's shared as package data (RData) rather than RDS, it will soon be pushed to the main branch of the package and I'll update the documentation in the present repo accordingly.
Since we were dealing with multiple species, we did not use the list from Deeke et al. directly, but simply queried the GO Cellular Component term (i.e. 'cytosolic ribosome'). This means that we use some more genes than they do, but considering their relative expression pattern I would doubt that this makes a big difference on the scaling factor.

[Martin-Fahrenberger]

Thank you for the quick response,
I m looking forward to running my own pipeline comparisons now :)

[plger]

great, let us know if there's any other issue or if you have comparison insights to share ;)