Gert Hulselmans

A `create_cistarget_track_databases.py` script will be added soon to this repo. It will use `bigWigAverageOverBed` to get the coverage in each of your regions and rank them.

When scoring the motifs for the species for which you lifted over regions from human, use `--fasta-original-species ORIGINAL_SPECIES_FASTA_FILENAME` as extra parameter (FASTA file with regions in human) so all regions...

Our SCENIC+ public motif collection is now available: https://resources.aertslab.org/cistarget/motif_collections/ moitf2TF snapshots can be found at: https://resources.aertslab.org/cistarget/motif_collections/v10nr_clust_public/snapshots/ To create annotation for other species try to find orthologs for your species for...

@KyleFerchen Also not all PWMs have a known or specific TF attached to it. Associating a PWM with the correct TF is a big challenge.

Not all PWMs listed in the motif to TF file are in the singletons directory as some motifs from different collections are exactly the same: ``` swissregulon__mm__Gfi1 = swissregulon__rn__Gfi1 =...

Hey Mark, Glad you liked the script. I added the `-C -` to curl.

Fixed. It now also will ask what to do when a file was already downloaded: ``` Do you want to (R)esume or re(S)tart the download or (C)ancel? ```

As you noticed, for now only directory shares are supported as that is how the NextCloud share links I get, are. I didn't use it myself, but it is possible...

Yeah, an option to enable this behavior (or print some warnings about `groupby` would be great.

It is never tested on Windows, so it likely wouldn't work. You could still try to run pySCENIC under WSL on Windows.