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malariagen / malariagen-data-python

Analyse MalariaGEN data from Python
https://malariagen.github.io/malariagen-data-python/latest/
MIT License
13 stars 23 forks source link

SNP browser to replace Panoptes #563

Open EricRLucas opened 2 weeks ago

EricRLucas commented 2 weeks ago

I tried to access the Panoptes web brower today, and found that it is being decommissioned.

I gazed upon its ruin, and I wept.

I gazed upon it some more, and I did wail, and beat my chest, and gnash my teeth.

It would be good to have some way in malariagen_data to put in a bunch of snp position and get information on snp effect, allele frequencies, and a plot with the genomic context for the snps. Something along the lines of the colab below, but less crap.

To the extent that there may be gems within with sewage, you are welcome to reuse that notebook. Also happy to help if needed.

https://colab.research.google.com/drive/1e8AI2PjZgIWLJyciz4h6TbYF4B_PBe59?usp=drive_link

leehart commented 1 week ago

Ref: https://github.com/cggh/panoptes

alimanfoo commented 1 week ago

Thanks @EricRLucas, this is the best issue that's ever been raised on GitHub 😆