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ccdmb / predector

Effector prediction pipeline based on protein properties.
Apache License 2.0
11 stars 7 forks source link

FEATURE REQUEST: Incorporate deepredeff into pipeline #37

Closed darcyabjones closed 3 years ago

darcyabjones commented 3 years ago

Deepredeff https://github.com/ruthkr/deepredeff/ has been on my radar for a while, but I haven't gotten around to trying it yet.

We need to evaluate it first because some of their numbers are a bit suspiciously good (I think it's just because their training data doesn't include a realistic negative set, i.e. their all like nuclear proteins so easier to distinguish than hydrophobins etc.). I'm sure it's fine but we'll see, especially while it's still un-reviewed.

Paper is here: https://www.biorxiv.org/content/10.1101/2020.07.08.193250v1.abstract

darcyabjones commented 3 years ago

Now published: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04293-3

darcyabjones commented 3 years ago

This was introduced with tag 1.2.0-beta