-
I have been using ember motifs for the network simulations with ~10K nodes using firefly NIC and merlin router. Now I am interested in simulating a complete HPC system by integrating the compute and m…
-
### Setup
Biopython 1.7.0, Python 2.7.13, and Mac OSX 10.12.6
I am trying to run the MEME parser on a file with protein motifs, but it returns a KeyError with 'X'.
The protein motifs occasional…
-
**Describe the bug**
I am running the grn part of the pyscenic through docker as exactly shared here ("https://pyscenic.readthedocs.io/en/latest/installation.html#command-line-interface"). The code …
-
Dear Authors,
It was mentioned in the paper that the
"Ultimately, our binding seed database was composed of approximately 250,000 helical motifs from which 140 million fingerprints were extracted…
-
Hello, and thanks for the nice R package.
I'm interested in using ShapeMotifEM, but am having trouble figuring out how to calculate performance metrics for the motifs it identifies. How would you rec…
-
* so we can re-use the same image prompts if required just modify the style (e.g. for several languages so we don't have the same images)
* this will just be a string we store somewhree central that …
-
Hello,
I'm wondering if anyone can assist with some issues I'm having re: locus assignment.
Some of my forward primers include ambiguous nucleotides (K, W, R, etc.) and some of the expected STR…
-
I've been running into trouble with GraphAligner recently on graphs that contain "universal" motifs. These are small graph components that have the right combination of edges and node sequences which …
-
Dear Jacob,
first thanks for all your work on the DNA model front!
I am aiming. to transfer pre-trained ChromBPNet models to PyTorch using from_chrombpnet() to fully leverage the tangermeme space.…
-
how can I visualize more than 10 motifs from MEME?
thanks for your useful package.