Dr Andrew Lonsdale

My first CRAN package! 🤓

Two of my favourite UpSet plot packages have been caught out by recent ggplot2 updates. That has cascaded into some Bioconductor packages failing (mine + others), so I figured I'd add another UpSet plot option to the mix. Hopefully this can help stabilise things a bit.

barbieQ: An R software package for analysing barcode count data from clonal tracking experiments https://www.biorxiv.org/content/10.1101/2025.09.11.675529v1

This year I came full circle to be the Faculty Advisor to COMBINE, the ISCB RSG for Australia (and @abacbs.bsky.social student subcommittee) — a group I was part of in the olden days.

It's mostly a hands-off role but my only (strong) advice so far? Get on BlueSky! So, welcome @combine1.bsky.social

ABACBS 2025 Conference Adelaide, South Australia. Nov. 24-

🚨 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

GitHub - Illumina/ExpansionHunter: A tool for estimating repeat sizes A tool for estimating repeat sizes. Contribute to Illumina/ExpansionHunter development by creating an account on GitHub.

The only other time I have noticed a PolyForm license is when we came across it looking at STR tools. Illumina updated ExpansionHunter to switch it from Apache to one of the PolyForm ones....

github.com/Illumina/Exp... ➡️ github.com/Illumina/Exp...

Every conference I have been involved with, I threaten that this will be the one where we do not extend abstracts.

Can you take that risk?

STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci - Genome Medicine Approximately 8% of the human genome consists of repetitive elements called tandem repeats (TRs): short tandem repeats (STRs) of 1–6 bp motifs and variable number tandem repeats (VNTRs) of 7 + bp moti...

The strchive.org paper is out!!
The paper describes STRchive as a resource to improve the diagnosis of tandem repeat disorders, then goes beyond it to consider what can be learned about childhood onset and population prevalence of these diseases.
🖥️ 🧬
link.springer.com/article/10.1...

Massive! Great work!

I know this is on brand for me to identify - the original link absorbed the 🎉 emoji!

Our paper benchmarking feature selection for scRNA-seq integration and reference usage is out now www.nature.com/articles/s41...!

Keep reading for more about how we did the study and what we found out 🧵 👇

1/16

"The thing about Carlton is they always try to walk it in" #afl #AFLTigersBlues

We are recruiting a group leader in laboratory research at Peter Mac Cancer Centre in
Melbourne, Australia 🔬🦘💥

Work in a cutting edge research environment in a vibrant world city!

We value research excellence, creativity and diversity.

Join us!

careers.petermac.org/job/MELBOURN...

Pleased to present our CITE-seq paper analysing 45 BAL samples from (un)treated children with CF and controls. BAL is a tricky tissue, 44 celltypes dominated by macrophages. Trailblazing analysis led by @jovmaksimovic.bsky.social @melanieneeland.bsky.social @shivanthans.bsky.social and collaborators

Thanks! If may have been when you were down under for the ABiC/ AGTA double if those talks were similar to that keynotes? It's been a while!

Question for @titus.idyll.org or 🧬 🖥️ if it triggers a recollection:

I've a vague memory of a (possibly) Titus blog/tweet/talk ~10yo of something like:

"Mucking around with computational infrastructure is great and all, but it isn't the *science*"

and can't find the source.

Flyer for CBA 2025, with link to main website: https://cancerbioinformatics.au/ and profile pictures of speakers: Jason Wong (University of Hong Kong) Jinmiao Chen (A*STAR) Nadia Davidson (WEHI) Joe Cursons (oNKo-innate Inc)

📣 Registrations and Abstract submissions are now open for Cancer Bioinformatics Australia 2025!

Abstracts, due 11th April: cancerbioinformatics.au/abstracts

Registration: cancerbioinformatics.au/register

Further info: cancerbioinformatics.au

See flyer for our amazing invited speakers!

#Rstats bsky.app/profile/did:...

Nextflow bsky.app/profile/did:...

Genomics/bioinfo 🧬🖥️ bsky.app/profile/did:...

Papers w/ code bsky.app/profile/did:...

RNA-seq bsky.app/profile/did:...

Biosecurity bsky.app/profile/did:...

Consgen bsky.app/profile/did:...

Genesky bsky.app/profile/did:...

(2/2)
Jan 2: Maybe the office will be quiet and I can get ahead.
Jan 6: Nice break, now back to it.
Jan 13: Respectable.
Jan 20: Batteries fully charged.
Jan 28: Must be nice.
Feb 4: Are you having a laugh?

(1/2)
In Australia, the end of year holiday period coincides with summer, several public holidays, and school holidays. Return date to work is best described as:

Dec 27: Keen. As. Mustard.
Jan 30: Might get bit of work done before New Year's Eve.

5th day:
“MINOR REVISIONS!!”

I call it #preprintmas

PIPING HOT DATA: Exporting editable ggplot graphics to PowerPoint with officer and purrr What, why, how, when, and who

officer/rvg are GREAT packages to export ggplot2 (R plots) to editable Powerpoint slides.

Saves me heaps time when I make plots for others: everybody wants to change a bunch of details. Now they do that themselves in Powerpoint with my 'base' plot.

www.pipinghotdata.com/posts/2020-0...

I will never cease trying to make #preprintmas happen, the happy time of year when great science gets pushed out the door to a preprint server before everyone takessome time off 🎁 📓

Save the Date for Cancer Bioinformatics Australia '25!

The 2nd CBA will be in Sydney on June 18th 2025.

Planning is well under way, with invited speakers including but not limited to @jwhwong.bsky.social and @nadia-davidson.bsky.social

See cancerbioinformatics.au for info and updates.

Damsel: analysis and visualisation of DamID sequencing in R AbstractSummary. DamID sequencing is a technique to map the genome-wide interaction of a protein with DNA. Damsel is the first Bioconductor package to prov

Happy to see our Damsel @bioconductor.bsky.social package published in Bioinformatics. Great work putting together this DamID sequencing and package from student Caitlin Page. Thanks to collaborators too @lonsbio.bsky.social

academic.oup.com/bioinformati...

Interesting that it has a crack, hallucinates what would be a very awesome tool (nf-core/metro-map), but then [checks notes] tells you how to do manually instead!

Ooo, that is nice. I did not have the time or skill and fell back to Carbon, but that keyboard shortcut is handy to know.

Great tool to help with Nextflow pipeline development!

If it could automatically create the @nf-co.re subway style pipeline plots for you that would be game over!

Ha of course! The Bio Data Zoo repo was perfect for what I needed for a talk.

I must apologise for, in haste, omitting a 42basepairs reference for the source of the data but will fix for future versions of that talk