Gert Hulselmans

@yanpinlu unfortenately I didn't hear anything back from them so far. In case it helps, our SCENIC+ public motif collection is now public: https://resources.aertslab.org/cistarget/motif_collections/ So at least you don't have...

https://github.com/JoGraesslin/Zebrafish_SCENIC @JoGraesslin provides his scripts at https://github.com/JoGraesslin/Zebrafish_SCENIC. A motif2tf table file with zebrafish names provided by him can be found at:[ https://drive.google.com/file/d/1__P8l-XTLA6Bup_ucKs4M1yGqE-wGbYz/view?usp=sharing](https://drive.google.com/file/d/1__P8l-XTLA6Bup_ucKs4M1yGqE-wGbYz/view?usp=sharing). It contains the human.tbl file with orthology names...

Our SCENIC+ public motif collection is now available: https://resources.aertslab.org/cistarget/motif_collections/

@jonhsussman You used the motif2TF file. The motif file should contain only 1 column with the motif IDs (Cluster-Buster motif filename basename without extension): ```bash cd v10nr_clust_public/singletons ls -1 *.cb...

The cross-species step is not necessarily required if you have enough motifs. You can run it with cross species with as closely related plant species as possible (under the assumption...

The `test.regions_vs_motifs.rankings.feather` file and `motifs-v10nr_clust-nr2.tgi-m0.01-o0.0.tbl` you can use with pySCENIC: https://pyscenic.readthedocs.io/en/latest/installation.html#docker-podman-and-singularity-apptainer-images Although for pySCENIC is would be better to use gene-based databases (`-g` option).

Yes, those should be sufficient.

You need to add `-g`, `--genes` argument: `-g '\|ENSSSCG[0-9]+$'`, but the original FASTA IDs still need to be unique, so probably you need to include the transcript ID too to...

You don't need liftOver as long as your expression matrix you generated for your RNAseq data has the same gene names as the ones you are generating now in the...

You need to convert the HGNC gene symbols in `motifs-v9-nr.hgnc-m0.001-o0.0.tbl` to the pig gene symbols that are in your database.