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aertslab / scenicplus

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
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Data base #435

Open SteveTur opened 3 months ago

SteveTur commented 3 months ago

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 commented 3 months ago

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 commented 3 months ago

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 commented 2 months ago

Hi @SteveTur

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