motif-clustering
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jvierstra
Clustering motif models to remove redundancy
Hello, I'm looking for the archetype models/consensus motifs in meme file format for version 1 but can't find it. Only version 2. Is there such a file somewhere?
Hi, your work is extremely good, and the example is quite good, but I still have some problems. In step 1: Compute pair-wise motif similarity,I wonder if it is necessary...
I see a lot of cases when a TF has motifs falling into distinct clusters. Is there a preferred strategy to select the likely correct WT motif for each TF...
Hi, I tried running your pipeline on my data, and I stumbled across some hard-coded paths in the code, e.g. `process_cluster.py` line 69 pointing to `/home/jvierstra/data/motifs/cluster/20181012/all.dbs.meme`, a file with all...
As in [here](https://resources.altius.org/~jvierstra/projects/motif-clustering-v2.0beta/all.dbs.meme) (5301 entries), but not [here](https://resources.altius.org/~jvierstra/projects/motif-clustering-v2.0beta/metadata.tsv) (5193 entries). These seem to be to be older, retired (?) motifs not included in current `JASPAR2022_CORE_non-redundant_pfms_meme.txt`. Solution would be to either...
