Ideas - Githubissues

fmicompbio / monaLisa

binned motif enrichment analysis and visualisation

https://fmicompbio.github.io/monaLisa/

GNU General Public License v3.0

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Ideas #1

Closed LukasBurger closed 5 years ago

LukasBurger commented 6 years ago

plot ATAC versus GC
scanning in R (no HOMER), Motif MA
enrichments (log2 fold-change instead of obs/exp)
stability selection

mbstadler commented 6 years ago

I added a generic function findMotifHits that uses "homer2 find" to identify motifs in sequences. Maybe the framework/interface can be also used for the non-homer based motif finding?

It conveniently accepts motifs in a file, PWMatrix or PWMatrixList, and sequences in a file, DNAString or DNAStringSet.

LukasBurger commented 6 years ago

great, thanks. Will have a look. I am currently implementing a simple log2 enrichment for the WMs as we discussed.

LukasBurger commented 6 years ago

-working on incorporating GC content of WMs into heatmap -row clustering of heatmap

mbstadler commented 5 years ago

Closed because it was broken into several independent issues