search

fmicompbio / monaLisa

binned motif enrichment analysis and visualisation
https://fmicompbio.github.io/monaLisa/
GNU General Public License v3.0
36 stars 6 forks source link

clustering of motifs #8

Closed LukasBurger closed 5 years ago

LukasBurger commented 5 years ago

Another thought which might be out of scope but is helpful for interpretation, many of these motifs are very similar (ex GATA and SP1), and might lead a researcher to think there is a ‘family’ effect when it really is just ambiguity due to sequence similarity. Possible something along the lines of similarity distance for the motifs? There are a few ways to calculate this and I know this would take some looking into, but just a thought.

LukasBurger commented 5 years ago

Can be solved by using HOMERs compareMotifs.pl function (uses Pearson correlation as similarity measure). I tested the function, works well. Could implement this pretty easily.

LukasBurger commented 5 years ago

done