[Biopython] Bioinformatics master's degree final project

[Ferran Fàbregas]

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 <alexeymorozov1991 at gmail.com>
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 <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
>> _______________________________________________
>> Biopython mailing list  -  Biopython at biopython.org
>> https://mailman.open-bio.org/mailman/listinfo/biopython
>>
>
>
> --
> Alexey Morozov,
> LIN SB RAS, bioinformatics group.
> Irkutsk, Russia.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20220103/b9cbf458/attachment-0001.htm>