Scenic-ArchR

[dimurali93]

Have anyone ever implemented scenic for Archr multiome?

[SeppeDeWinter]

Hi @dimurali93

There is no specific implementation for ArchR, however if you are able to extract count matrices and cistromes in the correct format and load it in python you can use the output.

See https://scenicplus.readthedocs.io/en/latest/faqs.html for some ideas.

Let me know if you get stuck somewhere.

Best,

Seppe

[LacquerHed]

Also trying to do this. I can export a dgcMatrix from an ArchR RangedSummarizedExperiment however this does not appear to be the proper format for creating a CistopicObject. Any tips on how to do this? Thanks.

[Umaarasu]

I am not sure about ArchR, but I recently exported seurat multiome for cisTopic tutorial mentioned in the FAQs to be used for scenic+ analysis. We need to input the count matrix as dataframe with cells as columns and regions as rows and can be obtained with this command "count_matrix <- as.data.frame(seuratObj@assays$ATAC@counts)" and metadata can be done obtained this command "metadata <- as.data.frame(seuratObj@active.ident)"

[bioarpit1]

hi Seppe

Thanks for the cool tool. The tutorial link you shared above is broken; I tried from here: https://pycistopic.readthedocs.io/en/latest/faqs.html as well, but that specific tutorial you mentioned has a broken link. Can you please direct me to the correct location?

Thanks

Arpit

[SeppeDeWinter]

Hi @bioarpit1

You can still find the tutorial here: https://github.com/aertslab/pycisTopic/blob/old/notebooks/Toy_melanoma-RTD.ipynb

Best,

Seppe