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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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Test data in scenicplus and pycisTopic jupyter notebook seem lost. #62

Closed wangmeijiao closed 1 year ago

wangmeijiao commented 1 year ago

Hi,

Here I report that test datasets (10x_multiome_brain_Seurat.loom and other input files) in both scenicplus (https://github.com/aertslab/scenicplus/blob/main/docs/Scenicplus_step_by_step-RTD.ipynb) and pycisTopic (https://pycistopic.readthedocs.io/en/latest/Single_sample_workflow-RTD.html) jupyter notebooks seem lost. Perhaps I miss some information within that notebook? I understand one can carry out seurat analysis from the downloaded dataset, but it would be great if the author can support a ready-to-use one ^_^. Thanks a lot!

Best, Meijiao

SeppeDeWinter commented 1 year ago

Hi @wangmeijiao

You can get the files from https://scope.aertslab.org/#/scenic-v2, press the little image "save" icon next to the file name (you can use this file HC_gene_based under 10x_multiome_brain -> SCENIC+).

image

They are the fully processed files, but they should contain everything to rerun the tutorial.

Best,

Seppe

wangmeijiao commented 1 year ago

Okey~, nice tool 'SCENIC+' by the way!