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aertslab / pycistarget

pycistarget is a python module to perform motif enrichment analysis in sets of regions with different tools and identify high confidence TF cistromes.
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motif_enrichment_homer disappear in version 1.0a2 #34

Open wangmeijiao opened 1 month ago

wangmeijiao commented 1 month ago

Dear Seppe,

The homer wrapper module has disappeared in the stable version 1.0.a2. This is useful for me to compare with my old homer results. I understand I can use this module in dev version (1.0.2.dev9+g0ed8289). But It will be handy to use in the stable version.

Thanks!

meijiao

wangmeijiao commented 1 month ago

Oh, besides, could you point to me the right homer tf motif meme file which can be loaded by pycistarget ? It was mentioned in the manual but not available.

wangmeijiao commented 1 month ago

The manual https://pycistarget.readthedocs.io/en/latest/pycistarget_chip-RTD.html#3.-Homer the meme file mentioned /staging/leuven/stg_00002/lcb/cbravo/Multiomics_pipeline/pycistarget_tutorial/scenicplus_motif_collection.meme