[Biopython] Bioinformatics master's degree final project

[Alexey Morozov]

Dear Ferran,

There is a Python library for GO enrichment called goenrich (
https://github.com/jdrudolph/goenrich). I haven't used it for the last
couple of years, but it did its job in 2018 or so (despite lacking some
tests available in eg topGO). OTOH, goenrich repo shows that the last
commit was in summer 2020, so maybe they've added something. Back when I
used it, BioPython integration was basically absent, they just used their
own objects for everything.

There is also a library called goatools (
https://github.com/tanghaibao/goatools), but I haven't actually used it, so
no comments.


пн, 3 янв. 2022 г. в 18:40, Ferran Fàbregas <ferri.fc at gmail.com>:

> Hi! My name is Ferran Fàbregas and I'm working on my bioinformatics
> master’s degree final project. I’m a computer scientist and a Python
> veteran but a BioPython newbie.
>
> I am writing this email because I would like to dedicate the final project
> of my master's degree in bioinformatics to the development of a library to
> implement gene annotation, pathway enrichment and access to gene ontologies
> from Python, similar to how it can be done in R using functions like
> enrichPathway from ReactomePA or enrichGo from ClusterProfiler.
>
> Have any tools been previously developed to do this using BioPython? Are
> there any packages similar to Bioconductor's OrgDb, ReactomePA , GOSeq or
> ClusterProfiler?
>
> I’m also working on a BioPython GUI based on PySide6. I've seen some old
> projects related to BioPython GUI development but seem to be discontinued.
>
> I would be very happy to use my time to contribute to the bioPython
> project, and I’m open to any suggestions or ideas.
>
> Thanks in advance,
>
> Ferran Fàbregas
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>


-- 
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.
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