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Agkm implementation, ic-based motif centering

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@AvantiShri AvantiShri released this 26 Aug 20:18
· 218 commits to master since this release

Corresponds to PR #63. Should fix some issues where modisco seems to produce very low-IC motifs; the problem was arising during motif post-processing when the motif was previously recentered around the region of highest average importance; this would sometimes go awry because the high average importance may have been driven by only a few seqlets; now, the motif centering is done based on information content.

There's also support for computing advanced gapped kmer embeddings (which work better than the regular gapped kmer embeddings and also use less memory), but it is still in pure python and I am looking at ways to speed it up.