Re: [Biopython] Bioinformatics master's degree final project

Thanks for your replies, it seems that the community prefers to use
different bioinformatics related modules for different functionalities
instead of one big, more complex module :)

A couple of questions about that:

Do you think that it makes sense adding some enrichment functions to
biopython?

Do you think that it can be useful to create a modular Python GUI that
integrates biopython functionalities plus Bioservices / GoEnrich / etc...
? Or maybe it is not useful at all because you can already use some servers
like the Galaxy project website (https://galaxyproject.org/)?

What do you think about that?

Thanks in advance,

F


On Mon, Jan 3, 2022 at 12:45 PM Alexey Morozov <[email protected]>
wrote:

> 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 <[email protected]>:
>
>> 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
>> _______________________________________________
>> Biopython mailing list  -  [email protected]
>> https://mailman.open-bio.org/mailman/listinfo/biopython
>>
>
>
> --
> Alexey Morozov,
> LIN SB RAS, bioinformatics group.
> Irkutsk, Russia.
>

_______________________________________________
Biopython mailing list  -  [email protected]
https://mailman.open-bio.org/mailman/listinfo/biopython