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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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Clarification request: what scRNA-seq data is needed to create the SCENIC+ object? #33

Closed liz-is closed 2 years ago

liz-is commented 2 years ago

I'm working through the tutorial here but with my own data that was processed with Seurat.

To facilitate modularity / interoperability, could you give a bit more detail about what data needs to be in the object provided as the GEX_anndata argument to create_SCENICPLUS_object()? From this line GEX_anndata = adata.raw.to_adata(), it looks like you're basically just passing in the original counts, but I haven't worked through the full scanpy processing so I'm not sure. Is there any other data that needs to be included in that object? (normalised data, PCA, etc...)

In general the tutorial is really nice and clear so far. Just for this purpose of interoperability with other tools, it would be super helpful to have a list up top with all the input data needed, so it's all in one place and easy for users to gather the necessary data in the right formats in advance.

cbravo93 commented 2 years ago

Hi @liz-is !

The only thing you need to provide is the count matrix and the cell data :). We normally use loom files when moving from/to R (ScopeLoomR), you can see an example here: https://scenicplus.readthedocs.io/en/latest/Scenicplus_step_by_step-RTD.html

Cheers!

C

liz-is commented 2 years ago

Fab, that's easy then - thanks a lot for the clarification!

Umaarasu commented 1 year ago

Hi @cbravo93 and @liz-is , do you have any examples to show how to export scRNA seq from R to Scenic+ without involving loom?

fahmadimoughari commented 4 months ago

Hi @liz-is !

The only thing you need to provide is the count matrix and the cell data :). We normally use loom files when moving from/to R (ScopeLoomR), you can see an example here: https://scenicplus.readthedocs.io/en/latest/Scenicplus_step_by_step-RTD.html

Cheers!

C

I need to use my Seurat and Signac objects for scenicplus. But the link that you provided in this comment does not exists anymore. Can you provide the new link?

SeppeDeWinter commented 4 months ago

Hi @fahmadimoughari

You can still find this notebook at this link: https://github.com/aertslab/scenicplus/blob/old/notebooks/Scenicplus_step_by_step-RTD.ipynb

Best,

Seppe