Josh L. Espinoza

Any preconfigured databases?

1

I'm looking for a method that can say whether an assembly is prokaryotic or eukaryotic. Was thinking this software might be helpful. Do you have any preconfigured databases that have...

This looks really awesome and would love to get started with this. Is there an official docs page?

Question: Unknown number of clusters?

2

Do you know if there have been any usage with an unknown number of clusters? Thanks for posting this btw! It makes a lot more sense looking at the code...

[Feature Request]: With statement usage for pandas functionality

3

Apologies for not using the template. I did not see a feature request option. https://stackoverflow.com/questions/40476680/how-to-use-tqdm-with-pandas-in-a-jupyter-notebook It would be really useful if we could move our code under a `with` statement...

[Question] Would clusters of proteins from MMSEQS2 be considered orthologs?

1

Let's say you had 100 strains of a particular species. If you did an all-vs-all clustering of proteins, would those resulting clusters be considered orthologs?

Is there an option for the maximum number of target seqs (similar to `--max-target-seqs` in `Diamond`)? I found this: ``` --max-seqs INT Maximum results per query sequence allowed to pass...

Is there an expected port for TensorFlow 2.0 and/or PyMC4?

8

First off...thank you SO SO MUCH for updating this code and porting it to some modern tools. This a huge resource for the community and especially someone like me who...

Nintendo Switch Pro controller not capture full range of joystick

1

I've downloaded the newest version: v2.5.9 and ran via command line. I've also used v2.5.8 from OpenEmu and the same issue exists. I know this isn't the case when running...

Random seed/state arguments for louvain and leiden

3

**Is your feature request related to a problem? Please describe.** Not necessarily **Describe the solution you'd like** Add random seed argument like in the following implementation: https://python-louvain.readthedocs.io/en/latest/api.html#community.best_partition **Describe alternatives you've...

Trying to run the examples at https://www.youtube.com/watch?v=fR5Wvb86-IU&feature=youtu.be but I'm getting the following error and I can't figure out how to fix it. Is it my `edward`, `numpy`, or `tensorflow` version?...