Data base

[SteveTur]

Hi everyone,

I just realized that my Snakemake pipeline step 3 isn't starting because of the ranking and score database. It seems that every time I download the ranking and the scores database from the resource link, the checksum never corresponds to yours.

Do you have any ideas on how to troubleshoot this?

Best,
Steven

[SeppeDeWinter]

Hi @SteveTur

Are you still able to load the databases?

from ctxcore.rnkdb import FeatherRankingDatabase
db = FeatherRankingDatabase(fname, name="test")
print(db.total_genes)

Best,

Seppe

[SteveTur]

Hi Seppe,

I've managed to get everything working, but I'm encountering issues with some of the post-analysis steps. It seems that I can't figure out how to plot the old GRN style from the previous version, and I don't think the perturbation functions are working in the new alpha version. Is it possible to get an example of how to use those tools with the new version of the alpha?

Best,

Steven

[SeppeDeWinter]

Hi @SteveTur

The perturbation simulation is now updated https://scenicplus.readthedocs.io/en/latest/Perturbation_simulation.html#Tutorial:-Perturbation-simulation