Feature request: Support for custom motif enrichment analysis

[AmosFong1]

Hello,

Thank you for developing and maintaining SnapATAC2. It's a great tool! Do you have any documentation on the pyDNAmotif class, or documentation on how to create custom motifs / region annotations? Are there plans to support this in the future?

Best,
Amos

[kaizhang]

Yes, this will be added.

[AmosFong1]

Hello @kaizhang,

That is great. Is there any recommended solution that I can try to work with for now? Perhaps specific source code to look at for pyDNAmotif? Specifically I want to define a pyDNAmotif instance for regions from an existing bed file.

Best,
Amos

[kaizhang]

If you have a meme motif file, you can use motifs = snapatac2._snapatac2.read_motifs(filename) to read the motifs.

[AmosFong1]

Hi @kaizhang, sounds good that’s a great option for PWM-based analysis. How about for performing enrichment test of a predefined set of genomic regions?