Philipp Bayer
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philippbayer.bsky.social
Philipp Bayer
@philippbayer.bsky.social
980 followers 1.2K following 990 posts
Bioinformatics / tech / books

'It is required that one man should goof gloriously for the people.'
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philippbayer.bsky.social
I finally caught an Excel-doing-dates in the wild!! Opened an SRA metadata sheet in Excel where the experiments were named 6-1, 6-2, 6-3, 8-1, 10-4 etc. and Excel did its thing
Excel putting dates into library names like 6-1
February 3, 2026 at 1:00 PM
philippbayer.bsky.social
was banging my head against a bug (VEP classifying my in-exon variants as 'downstream') that Claude Sonnet 4.5 fixed in about 5 minutes. I can understand the scepticism on LLMs being jammed into every corner of life, but there's merit in these tools
he VEP command looks correct, but the issue is that VEP is annotating based on ALL transcripts/features in the region, and "downstream_gene_variant" is being picked as the consequence. Since you didn't specify --pick or --pick_allele, VEP returns consequences for multiple transcripts, and your code is just taking the first one. Let me check how you're extracting the consequence from the VEP output: Found it! You're extracting only the second field from the CSQ column with map_chr(2). This is getting the consequence from the first transcript annotation, which might be a pseudogene or non-canonical transcript. Let me check what a VEP CSQ field actually contains: Perfect! I can see the issue now. The VEP CSQ field contains multiple transcript annotations separated by commas. The first annotation is for TSC2 (a different gene!) and shows "downstream_gene_variant". But if you look at the second annotation (after the first comma), you'll see it's for PKD1 ENST00000262304 and shows "3_prime_UTR_variant" for exon 46 (which is correct - exon 46 contains the 3' UTR). Your code is only extracting the consequence from the first transcript annotation (TSC2), not the PKD1 transcript! The fix is to parse all transcript annotations and filter for the PKD1 canonical transcript (ENST00000262304). Let me create the fix: PKD1_mutation_rate.qmd+24-1 Now let's test the fix by re-running the code to see if we get proper consequences for exons 40-46: Perfect! The fix worked! Now you're seeing proper consequences for exons 40-46: Missense variants (the most common)
February 3, 2026 at 1:46 AM
philippbayer.bsky.social
Went digging through the epstein files a bit and among the horrors it's always so frustrating how plain stupid these messages are.

You found alzheimers in plants in Monsanto data?!? Sure, man. Sure
Weird text message chain saying they found alzheimers in plants in Monsanto data Plants have 50 vaginas somehow
January 31, 2026 at 2:58 AM
philippbayer.bsky.social
Good luck to anyone applying for a DECRA!!!!
screenshot from the research office email announcing that DECRAs are open
January 30, 2026 at 3:09 AM
philippbayer.bsky.social
this is a beautiful album and you're all missing out
Ryo Fukui - Scenery
January 29, 2026 at 5:58 AM
philippbayer.bsky.social
Wooo level 8 on wanikani

(I've always refused to learn kanji and focused on vocabulary, but wow does it help to retain new Japaanese words when you know the underlying kanji meaning - 'well of course mortality means shibou. just look at the kanji's readings!')
Wanikani homepage level 8
January 29, 2026 at 3:58 AM
philippbayer.bsky.social
Brassicaceae at it again
Brassicaceae at it again
January 27, 2026 at 8:34 AM
philippbayer.bsky.social
In a world of darkness, a bright light shines
God awful ugly Lego crocs
January 24, 2026 at 2:45 AM
philippbayer.bsky.social
It has finally happened: qs was removed from CRAN. I only realised because I tried to build my fancy-pants targets pipeline from start

(the solution is to use qs2, but it seems like targets does not yet support qs2?)
#rstats
January 19, 2026 at 7:41 AM
philippbayer.bsky.social
But whyyyyyyy
Kanji: matsu, end. Visually almost the same as... Mi, not yet. The difference is the length of the horizontal bar in the middle
January 18, 2026 at 11:22 AM
philippbayer.bsky.social
I was studying Kanji and was wondering whether every single Kanji has the reading kou/コウ??
So I made a figure. Turns out, yes, kou/コウ is the most common reading in the Joyo kanji! but not by much
Pictured are how often the top 15 most common onyomi readings appear in the Joyo kanji.
January 10, 2026 at 10:01 AM
philippbayer.bsky.social
Libraries! Libraries! Libraries!!!!!
Three books - the book you wish your parents had read. Bowie's book shelf. The Gift.
January 4, 2026 at 5:28 AM
philippbayer.bsky.social
This place has 🎶wild horses🎶
January 1, 2026 at 12:08 AM
philippbayer.bsky.social
Happy new year from Japan!
January 1, 2026 at 12:04 AM
philippbayer.bsky.social
Small cultural victory for Australia - found a Bluey gacha!
Bluey gacha!
December 24, 2025 at 11:56 AM
philippbayer.bsky.social
I'm in Japan! They lost my luggage! Good start!
December 22, 2025 at 5:50 AM
philippbayer.bsky.social
Let me put of this prison of my own construction
December 20, 2025 at 12:55 AM
philippbayer.bsky.social
Last day officially being employed!
Back to being employed 5th January...
A beach
December 19, 2025 at 1:15 AM
philippbayer.bsky.social
Had my farewell tea with OceanOmics today... beautiful words and amazing farewell gifts!! Very emotional
December 15, 2025 at 7:37 AM
philippbayer.bsky.social
#eDNA postdoc opportunity in Qatar.
'Environmental DNA (eDNA) & Marine Mammals Monitoring'

Got it via email and can't find a public link, yet?
December 2, 2025 at 3:54 AM
philippbayer.bsky.social
My new strawberry is having its first fruit and it's an absolute Yog-Sothoth of a fruiting body. Just unwell in non-euclidian space
weird-ass strawberrry
November 24, 2025 at 12:22 AM
philippbayer.bsky.social
The local library had the good stuff!!!! Smack bang in the middle of the 'new arrivals'
@chucktingle.bsky.social thank you for writing
November 17, 2025 at 10:28 AM
philippbayer.bsky.social
git is a normal tool
filter-branch comes with a pile of caveats (more on that below) even once you figure out the necessary invocation(s): git filter-branch \ --tree-filter 'mkdir -p my-module && \ git ls-files \ | grep -v ^src/ \ | xargs git rm -f -q && \ ls -d * \ | grep -v my-module \ | xargs -I files mv files my-module/' \ --tag-name-filter 'echo "my-module-$(cat)"' \ --prune-empty -- --all git clone file://$(pwd) newcopy cd newcopy git for-each-ref --format="delete %(refname)" refs/tags/ \ | grep -v refs/tags/my-module- \ | git update-ref --stdin git gc --prune=now Some might notice that the above filter-branch invocation will be really slow due to using --tree-filter; you could alternatively use the --index-filter option of filter-branch, changing the above commands to: git filter-branch \ --index-filter 'git ls-files \ | grep -v ^src/ \ | xargs git rm -q --cached; git ls-files -s \ | sed "s%$(printf \\t)%&my-module/%" \ | git update-index --index-info; git ls-files \ | grep -v ^my-module/ \ | xargs git rm -q --cached' \ --tag-name-filter 'echo "my-module-$(cat)"' \ --prune-empty -- --all git clone file://$(pwd) newcopy cd newcopy git for-each-ref --format="delete %(refname)" refs/tags/ \ | grep -v refs/tags/my-module- \ | git update-ref --stdin git gc --prune=now
November 3, 2025 at 5:39 AM
philippbayer.bsky.social
Underlying the sightings is automated curation of species sightings based on Aquamaps and Fishbase, we're erring on the side of caution; species detected but not supported in the area are not included.
October 23, 2025 at 11:06 AM
philippbayer.bsky.social
- Beautiful image gallery of detected species courtesy of MarineWise
- AI-summary of species of human interest
- Graphical visualisation of species habitats, food sources, and phylogenetic diversity
October 23, 2025 at 11:06 AM