Gert Hulselmans

`/../PY_SCENIC/TRIAL_PY/Trial_meta_adj.tsv` is a weird notation for `/PY_SCENIC/TRIAL_PY/Trial_meta_adj.tsv`. Didn't you mean: `./../PY_SCENIC/TRIAL_PY/Trial_meta_adj.tsv` ?

See: https://github.com/aertslab/pySCENIC/issues/579#issuecomment-2405207860

You can always load a conda environment from a bash script.

You can always checkout any commit you want, not that I recommend using such an old version: ```bash git clone https://github.com/aertslab/scenicplus cd scenicplus # Checkout commit of your choice. git...

Some motifs were removed as they had wrong motif to TF annotations in the source motif collection.

Can you try? ```bash arboreto_with_multiprocessing.py --num_worker 4 --sparse --method grnboost2 -o sce.adj.csv sample.loom hs_hgnc_tfs.txt ```

Install an older version of numpy.

Or use the Docker/Podman/Singularity/Apptainer images: https://pyscenic.readthedocs.io/en/latest/installation.html#docker-podman-and-singularity-apptainer-images

numpy 2.0 deprecated a lot of the old numpy API, so it is likely to give a lot of issues. Downgrade to a 1.x version. If you use the latest...

Can you with try with the Docker/Podman/Singularity/Apptainer images instead? https://pyscenic.readthedocs.io/en/latest/installation.html#docker-podman-and-singularity-apptainer-images