search

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.
Other
176 stars 28 forks source link

Provide files used for tutorial SCENIC+ step-by-step in the human cerebellum #35

Closed chrarnold closed 2 years ago

chrarnold commented 2 years ago

I am following the tutorial SCENIC+ step-by-step in the human cerebellum, and I dont see where the linked file /staging/leuven/stg_00002/lcb/cbravo/Multiomics_pipeline/analysis/10x_multiome_brain/output/atac/pycistopic/DARs/Imputed_accessibility.pklis available anywhere. The same goes for /staging/leuven/stg_00002/lcb/cbravo/Multiomics_pipeline/analysis/10x_multiome_brain/output/atac/pycistopic/10x_multiome_brain_cisTopicObject_noDBL.pkl, /staging/leuven/stg_00002/lcb/cbravo/Multiomics_pipeline/analysis/10x_multiome_brain/output/rna/seurat/10x_multiome_brain_Seurat.loom, and the various files within /staging/leuven/stg_00002/lcb/cbravo/Multiomics_pipeline/analysis/10x_multiome_brain/output/atac/pycistarget/.

Alternatively, the SCENIC+ object could be made available so one can start from there, maybe?

Is it possible to provide these files somewhere so the vignette can be followed directly, have I overseen it? Thanks!

cbravo93 commented 2 years ago

Hi @chrarnold !

I have put the SCENIC+ object here (it has the complete analysis, it is big!): https://drive.google.com/file/d/1YdEc6eSR4QhzQ1xx13ASSQ9cKzKfT5l_/view?usp=sharing . You can also generate those files yourself running the whole SCENIC+ workflow, following the pycisTopic (https://pycistopic.readthedocs.io/en/latest/Single_sample_workflow-RTD.html) and pycistarget (https://pycistarget.readthedocs.io/en/latest/pycistarget_scenic%2B_human_brain.html) tutorials. If you want to query regulons or visualize the data, you can take a look in https://scope.aertslab.org/#/scenic-v2/ (under 10x_multiome_brain).

Cheers!

C

chrarnold commented 2 years ago

Thanks a lot for the super-quick reply and the link! Appreciated, cheers!

bitcometz commented 1 year ago

hello, I also want those files to run SCENIC+ because I failed at pycisTopic with peak calling.

But I can not open the URL:

https://drive.google.com/file/d/1YdEc6eSR4QhzQ1xx13ASSQ9cKzKfT5l_/view?usp=sharing

Could you please help with this problem ? @chrarnold Thanks very much !!!

Thanks !!!