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Reposted by Dr Andrew Lonsdale

Stevie Ped @smped.bsky.social · 2d

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.

CRAN Updates @cranupdates.bsky.social · 2d

New on CRAN: SimpleUpset (0.1.2). View at https://CRAN.R-project.org/package=SimpleUpset

SimpleUpset: Create Upset Plots

Create Upset plots using a combination of 'ggplot2' and 'patchwork'.

CRAN.R-project.org

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Reposted by Dr Andrew Lonsdale

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 24d

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

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Dr Andrew Lonsdale @lonsbio.bsky.social · Aug 28

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

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Reposted by Dr Andrew Lonsdale

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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Dr Andrew Lonsdale @lonsbio.bsky.social · Jun 5

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...

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.

github.com

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Dr Andrew Lonsdale @lonsbio.bsky.social · Apr 11

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?

Cancer Bioinformatics Australia @cancerbioinfoau.bsky.social · Apr 11

⚠️ ONE HOUR TO GO ⚠️

Cancer Bioinformatics Australia @cancerbioinfoau.bsky.social · Apr 9

2 Days left!! 🏃
It's time to get your abstracts reviewed and submitted! 🚀
Closing this Friday, 11th of April at 5:00PM AEST (or 3:00PM AWST 😛)
cancerbioinformatics.au/abstracts

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Reposted by Dr Andrew Lonsdale

Harriet Dashnow @hdashnow.bsky.social · Mar 26

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...

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...

link.springer.com

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Dr Andrew Lonsdale @lonsbio.bsky.social · Mar 20

Massive! Great work!

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Dr Andrew Lonsdale @lonsbio.bsky.social · Mar 20

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

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Reposted by Dr Andrew Lonsdale

Luke Zappia @lazappi.bsky.social · Mar 18

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 🧵 👇

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https://www.nature.com/articles/s41592-025-02624-3🎉

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Dr Andrew Lonsdale @lonsbio.bsky.social · Mar 13

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

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Reposted by Dr Andrew Lonsdale

Ben Hogan @benjhogan.bsky.social · Mar 5

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...

Group Leader

careers.petermac.org

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Reposted by Dr Andrew Lonsdale

Alicia Oshlack @aliciao.bsky.social · Mar 1

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

medRxivpreprint @medrxivpreprint.bsky.social · Feb 27

Single-cell atlas of BAL from preschool cystic fibrosis reveals key inflammatory pathways modified by the CFTR modulator ivacaftor in the early life lung. https://www.medrxiv.org/content/10.1101/2025.02.24.25322508v1

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Dr Andrew Lonsdale @lonsbio.bsky.social · Mar 1

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!

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Dr Andrew Lonsdale @lonsbio.bsky.social · Feb 25

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.

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Reposted by Dr Andrew Lonsdale

Cancer Bioinformatics Australia @cancerbioinfoau.bsky.social · Feb 25

📣 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!

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Dr Andrew Lonsdale @lonsbio.bsky.social · Feb 18

a woman is sitting in a living room talking to someone and says " i mean it 's one banana "

Alt: Arrested Development GIF: Lucille Bluth sitting in a living room talking to someone and says " I mean it's one banana Michael. What could it cost? 10 dollars?"

media.tenor.com

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Reposted by Dr Andrew Lonsdale

Stephen Turner @stephenturner.us · Feb 4

#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:...

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Dr Andrew Lonsdale @lonsbio.bsky.social · Jan 8

(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?

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Dr Andrew Lonsdale @lonsbio.bsky.social · Jan 8

(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.

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Dr Andrew Lonsdale @lonsbio.bsky.social · Dec 23

5th day:
“MINOR REVISIONS!!”

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Dr Andrew Lonsdale @lonsbio.bsky.social · Dec 23

I call it #preprintmas

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Reposted by Dr Andrew Lonsdale

Philipp Bayer @philippbayer.bsky.social · Dec 18

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...

PIPING HOT DATA: Exporting editable ggplot graphics to PowerPoint with officer and purrr

What, why, how, when, and who

www.pipinghotdata.com

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Dr Andrew Lonsdale @lonsbio.bsky.social · Dec 19

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 🎁 📓

Dr Andrew Lonsdale @lonsbio.bsky.social · Dec 14

Last year I noticed that a lot of of great bioinformatics / comp bio papers ended up on biorxiv etc just before the end of year holidays... so if you see more this year, be sure to mention preprintmas to find them all! 🎁 📓

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Reposted by Dr Andrew Lonsdale

Cancer Bioinformatics Australia @cancerbioinfoau.bsky.social · Dec 15

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.

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