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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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Step by step pipeline #366

Closed SteveTur closed 7 months ago

SteveTur commented 7 months ago

Hello,

We started our project using the step-by-step pipeline, which worked well on our datasets. However, we have not found back those tutorials since the update.

Since we start all of our analysis with it, we would like to use it for the rest of our sample.

Do you plan to put them back?

Best,

Steven

jesswhitts commented 7 months ago

They're in the 'old' branch of this github repo, if you go to 'notebooks' you can download the old tutorials

SteveTur commented 7 months ago

Thank you so much! Is everything will work as before or do we need to update scenicplus?

jesswhitts commented 7 months ago

If you've got the previous version installed already, you should be able to follow the previous tutorials without updating. If you update to the new one you'll need to follow the new tutorials as the code is quite different.

SeppeDeWinter commented 7 months ago

I second what @jesswhitts is saying ;)

Good luck with your analysis @SteveTur.

Best,

Seppe