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Reposted by Feargal Ryan

Darren Dahly @statsepi.bsky.social · 8d

Carefully reading the papers you cite is like a superpower. You might be surprised what you actually find! 😜

Feargal Ryan @feargalr.bsky.social · 8d

Fascinating! Genetic risk factors for disease susceptibility show little association with disease progression/mortality. Important as most individuals only approach the health care system after developing symptoms. #genomics

www.nature.com/articles/s41...

Limited overlap between genetic effects on disease susceptibility and disease survival - Nature Genetics

Systematic comparison of genome-wide association results for disease risk and disease-specific mortality for nine common diseases across seven biobanks finds limited overlap between genetic effects on disease susceptibility and survival.

www.nature.com

Reposted by Feargal Ryan

Microbiome Virtual International Forum @microbiomevif.bsky.social · 9d

#MVIF Season 5!

Microbiome Virtual International Forum @microbiomevif.bsky.social · 27d

#MVIF Season 5 has started!

Check out the program and
feel free to join the keynotes by presenting your work–abstract submission is open:
www.microbiome-vif.org/en-US/-/info...

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Feargal Ryan @feargalr.bsky.social · Sep 8

Caught the lunar eclipse up in the Flinders Ranges!

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Reposted by Feargal Ryan

Altmetric @altmetric.com · Sep 7

WANT

publishorperish.games

Publish or Perish: A Humorous Party Game about Academic Publish

Welcome to the chaotic life of academic publishing. In this game, you are a clueless researcher trying to do the one and only thing that matters in your academic life: churning out publications, fast....

publishorperish.games

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Reposted by Feargal Ryan

abacbs.bsky.social @abacbs.bsky.social · Sep 5

ECRs, join us on Sept 30th 2025, 3-4:30pm for our online Career Panel Q&A Session on bioinformatics career pathways within academia and industry. Check out our invited speakers below! Register at shorturl.at/Lerzw

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Feargal Ryan @feargalr.bsky.social · Aug 19

Replied above with a link to how I did it on GitHub!

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Feargal Ryan @feargalr.bsky.social · Aug 19

FYI finally tidied this up into something usable github.com/feargalr/bac...

GitHub - feargalr/bacdive_harvester: R tools for scraping and extracting bacterial data from the BacDive database (Bacterial Diversity Metadatabase)

R tools for scraping and extracting bacterial data from the BacDive database (Bacterial Diversity Metadatabase) - feargalr/bacdive_harvester

github.com

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Reposted by Feargal Ryan

abacbs.bsky.social @abacbs.bsky.social · Aug 14

🚨 Less than 48 hours left! 🚨
Abstract submissions for #ABACBS2025 close midnight Friday, Aug 15 — no extensions.

www.abacbs.org/abacbs2025

ABACBS 2025 Conference

Adelaide, South Australia. Nov. 24-

www.abacbs.org

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Feargal Ryan @feargalr.bsky.social · Aug 7

PS shoot me a DM if you want the code I used?. I'll put it together into a GitHub repo but that might not be for a few weeks while I'm busy with other bits.

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Feargal Ryan @feargalr.bsky.social · Aug 7

Mostly fine once I had spent the time to look up a bunch of different bacteria to get a feel for what different entries look like. That was time consuming. Initially I had planned to use an LLM (either local or via the ChatGPT API) to scrape the data I needed but they all kept making things up 😅

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Feargal Ryan @feargalr.bsky.social · Aug 7

Drop me a line if you want to know more. The methodology was also published in Briefings in Bioinformatics earlier this year academic.oup.com/bib/article/...

TaxSEA: rapid interpretation of microbiome alterations using taxon set enrichment analysis and public databases

Abstract. Microbial communities are essential regulators of ecosystem function, with their composition commonly assessed through DNA sequencing. Most curre

academic.oup.com

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Feargal Ryan @feargalr.bsky.social · Aug 7

Link to BioConductor - bioconductor.org/packages/dev...

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Feargal Ryan @feargalr.bsky.social · Aug 7

Just about to push a big update to our R package TaxSEA where we've spent a lot of time collating data from the BacDive database so it's readily usable in a metagenomics analysis. See example below from the HMP IBD data. #metagenomics #bioinformatics #microbiome #microbiota

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Reposted by Feargal Ryan

abacbs.bsky.social @abacbs.bsky.social · Aug 5

🚨 Abstract deadline extended! 🚨

You’ve now got until August 15 to submit for #ABACBS2025 — one-time extension only!
Join us in Adelaide for world-class #bioinformatics, workshops, student & EMCR events, and more.

🔗 www.abacbs.org/abacbs2025

ABACBS 2025 Conference

Adelaide, South Australia. Nov. 24-

www.abacbs.org

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Reposted by Feargal Ryan

mmarchin.bsky.social @mmarchin.bsky.social · Jul 24

@hubertr.bsky.social‬ presented during #bioinfocore about GEO uploader, trying to simplify the upload process for researchers (I kinda hate doing this, so I'll be looking at it) github.com/fgcz/geo-upl... #ISMBECCB2025

GitHub - fgcz/geo-uploader: A Python GUI for the upload of NGS data to GEO

A Python GUI for the upload of NGS data to GEO. Contribute to fgcz/geo-uploader development by creating an account on GitHub.

github.com

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Feargal Ryan @feargalr.bsky.social · Jul 23

Tomorrow at 9:40am I’ll be speaking at #ISMBECCB2025 about how we can speed up microbiome data interpretation using taxon sets

Paper: academic.oup.com/bib/article/...

R package on #Bioconductor: TaxSEA
#RStats #Microbiome

Come say hi, I flew from Australia for this 🤣

TaxSEA: rapid interpretation of microbiome alterations using taxon set enrichment analysis and public databases

Abstract. Microbial communities are essential regulators of ecosystem function, with their composition commonly assessed through DNA sequencing. Most curre

academic.oup.com

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Reposted by Feargal Ryan

abacbs.bsky.social @abacbs.bsky.social · Jul 2

Finally joined Bluesky! Follow along to stay connected with ABACBS. Keep an eye out in the coming days, we’ll be releasing more details for 2025 conference, including opening abstract submissions and announcing invited speakers!

www.abacbs.org/abacbs2025

ABACBS 2025 Conference

Adelaide, South Australia. Nov. 24-

www.abacbs.org

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Reposted by Feargal Ryan

Microbiome Virtual International Forum @microbiomevif.bsky.social · May 19

⭐️Microtalks:
🇺🇸 @michaelwasney.bsky.social
🇯🇵 Yiting Liu

⭐️Keynote:
🇦🇺 Emad El-Omar

⭐️Selected talks:
🇦🇺 Chaoran Yang
🇦🇺 @feargalr.bsky.social‬
🇨🇦 @vdumeaux.bsky.social

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Feargal Ryan @feargalr.bsky.social · Apr 22

Please do!

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Feargal Ryan @feargalr.bsky.social · Apr 22

Manuscript out now in Briefings in Bioinformatics!

TaxSEA: rapid interpretation of microbiome alterations using taxon set enrichment analysis and public databases. #microbiome #metagenomics
academic.oup.com/bib/article/...

Feargal Ryan @feargalr.bsky.social · Apr 17

My first R package is officially out Bioconductor 3.21 today 🎉
TaxSEA adapts GSEA-style methods for metagenomic data— useful for interpreting differential abundance results. Manuscript accepted & in-press. Check it out bioconductor.org/packages/rel...
#Bioinformatics #Metagenomics #RStats

TaxSEA

TaxSEA is an R package for Taxon Set Enrichment Analysis, which utilises a Kolmogorov-Smirnov test analyses to investigate differential abundance analysis output for whether there are alternations in ...

bioconductor.org

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Reposted by Feargal Ryan

Svetlana Ugarcina Perovic @svetlanaup.bsky.social · Apr 17

argNorm is published now academic.oup.com/bioinformati...

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Feargal Ryan @feargalr.bsky.social · Apr 17

Maybe I’ve been spending too much time analysing data, but I actually found building this… fun? 😂
More info + preprint link below.

github.com/feargalr/Tax...

#Bioinformatics #Metagenomics #TaxSEA #RStats

GitHub - feargalr/TaxSEA: Taxon Set Enrichment Analysis

Taxon Set Enrichment Analysis. Contribute to feargalr/TaxSEA development by creating an account on GitHub.

github.com

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Feargal Ryan @feargalr.bsky.social · Apr 17

My first R package is officially out Bioconductor 3.21 today 🎉
TaxSEA adapts GSEA-style methods for metagenomic data— useful for interpreting differential abundance results. Manuscript accepted & in-press. Check it out bioconductor.org/packages/rel...
#Bioinformatics #Metagenomics #RStats

TaxSEA

TaxSEA is an R package for Taxon Set Enrichment Analysis, which utilises a Kolmogorov-Smirnov test analyses to investigate differential abundance analysis output for whether there are alternations in ...

bioconductor.org

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Feargal Ryan @feargalr.bsky.social · Apr 11

Excellent editorial in Microbiome this week including lots of practical advice for analysis (and lots of what not to do!) #microbiome #bioinformatics

microbiomejournal.biomedcentral.com/articles/10....

A blueprint for contemporary studies of microbiomes - Microbiome

This editorial piece co-authored by the Senior Editors at Microbiome aims to highlight current challenges in the field of environmental and host-associated microbiome research. We also take the opport...

microbiomejournal.biomedcentral.com

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