<div dir="ltr"><div>Dear Ferran,</div><div><br></div><div>There is a Python library for GO enrichment called goenrich (<a href="https://github.com/jdrudolph/goenrich">https://github.com/jdrudolph/goenrich</a>). 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. </div><div><br></div><div>There is also a library called goatools (<a href="https://github.com/tanghaibao/goatools">https://github.com/tanghaibao/goatools</a>), but I haven't actually used it, so no comments.<br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">пн, 3 янв. 2022 г. в 18:40, Ferran Fàbregas <<a href="mailto:ferri.fc@gmail.com">ferri.fc@gmail.com</a>>:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div class="gmail_default" style="font-size:small"><span id="gmail-m_4545923348532060833gmail-docs-internal-guid-83de775a-7fff-2e58-d1b9-f42527534b29"><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-variant-numeric:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap">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.</span></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-variant-numeric:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap">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.</span></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-variant-numeric:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap">Have any tools been previously developed to do this using BioPython? Are there any packages similar to Bioconductor's OrgDb, ReactomePA , GOSeq or ClusterProfiler?</span></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-variant-numeric:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap">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.</span></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-variant-numeric:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap">I would be very happy to use my time to contribute to the bioPython project, and I’m open to any suggestions or ideas.</span></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-variant-numeric:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap">Thanks in advance,</span></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-variant-numeric:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap">Ferran Fàbregas</span></p></span></div></div>
_______________________________________________<br>
Biopython mailing list  -  <a href="mailto:Biopython@biopython.org" target="_blank">Biopython@biopython.org</a><br>
<a href="https://mailman.open-bio.org/mailman/listinfo/biopython" rel="noreferrer" target="_blank">https://mailman.open-bio.org/mailman/listinfo/biopython</a><br>
</blockquote></div><br clear="all"><br>-- <br><div dir="ltr" class="gmail_signature"><font face="arial,helvetica,sans-serif">Alexey Morozov,<br>LIN SB RAS, bioinformatics group.<br>Irkutsk, Russia.<br></font></div>