Gert Hulselmans

Are the gene IDs in your database exactly the same as in human (also same casing)? ```python import cistarget_db ctx_rankings_genes_vs_motifs_feather_file = 'your_file.*.feather' gene_ids = cistarget_db.CisTargetDatabase.get_all_region_or_gene_ids_and_motif_or_track_ids_from_db(ctx_rankings_genes_vs_motifs_feather_file)[1] print(gene_ids) gene_ids.ids ```

That is probably not the best idea, unless you also want to change your input expression matrix every time.

You can do that with Ensembl Biomart. Example for human to mouse mapping: ``` # Map Ensembl gene IDs to HGNC or MGI symbols. # Filename: ensg_to_hgnc.ensembl${ensembl_version}.tsv # * Dataset:...

yes.

It will be the same as the `motifs_vs_genes.rankings.feather` matrix is transposed to make `genes_vs_motifs.rankings.feather` If you really want, you can generate it with: ```python import cistarget_db m_vs_g_ct_db = cistarget_db.read_db("motifs_vs_genes.rankings.feather") g_vs_m_ct_db...

For pySCENIC you only will need `zf.genes_vs_motifs.rankings.feather`. Cross-species it not necessary nowadays as it was in the past as we have way more motifs than we had in the past.

SCENIC is deprecated, use pySCENIC instead: https://pyscenic.readthedocs.io/en/latest/installation.html#docker-podman-and-singularity-apptainer-images pySCENIC does not need `org` as you just give a motif to TF annotation file with zebrafish genes as argument in the `ctx`...

> while running the script, it shows the following for several genes. `2023-07-24 12:48:01,796 - pyscenic.transform - WARNING - Less than 80% of the genes in Regulon for si:dkey-253d23.9 could...

The motifs need to be in Cluster-Buster format. The following function will create them (put one homer motif per file). ```bash homer_to_clusterbuster () { local homer_motif_file="${1}"; awk -F '\t' -v...

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