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Mentions
@fooliu @nilshomer @lh3lh3 (9) homer2-ao: A pair of speedups to the homer2 motif discovery and scanning algorithms making them 10-100x faster and use a small fraction of the memory. Released ourselves as-is because the authors were not responsive, but all credit should go to them. jmschrei/homer2-ao
Finally, for the detail-oriented among you (👀 @nv1ctus), the figwig file format comes with a formal Kaitai Struct specification that describes what a figwig actually *is*. figwig#23
The week of drops continues: this time, the figwig data format for genomics! figwig generalizes bigwigs to n-dimensional arrays, so can efficiently store huge sets of tracks, single-cell experiments, fiber-seq, and even Hi-C and scHi-C experiments. jmschrei/figwig
Second: A fused Cherimoya DeepLIFT has been merged and a new release (v0.3.1) is out. ~7x faster DeepLIFT for models of the same size. This was a huge bottleneck, even with a lightweight model. Thanks @eugmattei for the excellent PR! cherimoya#104
A comprehensive description is on the PR. Hope ya'll find it useful! tangermeme#120