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Reposted by Luke Zappia

James Bonfield @jbonfield.bsky.social · 24d

Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.

Ie: it's not us (Samtools team)! Be warned

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Reposted by Luke Zappia

Stephen Turner @stephenturner.us · Aug 29

anndataR enables seamless R-Python interoperability for single-cell RNA-seq by reading, writing, and converting H5AD files, supporting Seurat and SingleCellExperiment formats www.biorxiv.org/content/10.1... 🧬🖥️🧪 #Rstats github.com/scverse/annd...

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Reposted by Luke Zappia

Louise Deconinck @louisedck.bsky.social · Aug 25

A very big thank you to all co-authors and collaborators! @lazappi.bsky.social @rcannood.bsky.social Martin Morgan @scverse.bsky.social @ivirshup.bsky.social Chananchida Sang-aram Danila Bredikhin Brian Schilder Ruth Seurinck @yvansaeys.bsky.social @saeyslab.bsky.social

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Luke Zappia @lazappi.bsky.social · Aug 26

Hopefully coming soon to @bioconductor.bsky.social!

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Luke Zappia @lazappi.bsky.social · Aug 26

It's taken more than 2 years but we can officially announce anndataR!

There's still a lot of features to add but we hope a robust, "official", R-native H5AD reader/writer will unlock the defacto single-cell storage format for R users by avoiding issues with current solutions like zellkonverter.

Louise Deconinck @louisedck.bsky.social · Aug 25

We're excited to share that our preprint on anndataR, a new package bringing Python's AnnData to R, is now available on bioRxiv 🎉

🔗 Read the paper: www.biorxiv.org/content/10.1...
💻 Check the package in action: anndatar.data-intuitive.com

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Reposted by Luke Zappia

Louise Deconinck @louisedck.bsky.social · Aug 25

We're excited to share that our preprint on anndataR, a new package bringing Python's AnnData to R, is now available on bioRxiv 🎉

🔗 Read the paper: www.biorxiv.org/content/10.1...
💻 Check the package in action: anndatar.data-intuitive.com

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Reposted by Luke Zappia

David Shiffman, Ph.D. 🦈 @whysharksmatter.bsky.social · Jun 17

This week in my graduate-level Science Communication course, we are discussing communicating science to the public through public speaking (i.e., museum "evening with a scientist" nights, Nerd Nite lectures, speaking at community events, etc).

What advice do you have to share with my students? 🧪

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Reposted by Luke Zappia

Michael Love @mikelove.bsky.social · May 30

Bioconductor moving to Zulip for community chat

stat.ethz.ch/pipermail/bi...

[Bioc-devel] Bioconductor is moving from Slack to Zulip – 2 June

stat.ethz.ch

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Reposted by Luke Zappia

Marnie Blewitt @marnieblewitt.bsky.social · May 13

www.wehi.edu.au/careers/make...
WEHI is looking for new lab heads! New and experienced lab heads welcome. Check out the ad, consider applying and share. We’re a collaborative bunch, in Australia, with fabulous technology, great colleagues at a values-driven organisation. @wehi-research.bsky.social

Make your future Melbourne | WEHI

Lead the next wave of biomedical discovery

www.wehi.edu.au

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Lisa Sikkema @lisasikkema.bsky.social · Jun 3

Analyzing your single-cell data by mapping to a reference atlas? Then how do you know the mapping actually worked, and you’re not analyzing mapping-induced artifacts? We developed mapQC, a mapping evaluation tool www.biorxiv.org/content/10.1... from the ‪@fabiantheis lab. Let’s dive in🧵

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Reposted by Luke Zappia

Matthias Stahl @higsch.com · May 27

We digitized the AfD report of the Federal Office for the Protection of the Constitution.

This (secret) document was created to deliver proofs for the party‘s extreme right nature.

Now you can explore it interactively.

➡️ 🎁 🇩🇪 www.spiegel.de/politik/deut...

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Reposted by Luke Zappia

Yvan Saeys @yvansaeys.bsky.social · May 1

🔥 Just published! Thrilled to share that our work on funkyheatmap has just been published in the Journal of Open Source Software 🎉

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Reposted by Luke Zappia

khrovatin.bsky.social @khrovatin.bsky.social · Apr 28

There is no reason to stay bound to one programming language. I discussed ways to ease R-Python interoperability with Luke Zappia, Philipp Angerer, Tomasz Kalinowski.
Their tips and tricks are collected in this blog: hrovatin.github.io/posts/r_pyth...
@lazappi.bsky.social @t-kalinowski.bsky.social

From R to Python with minimal baggage

Getting the best of both worlds.

hrovatin.github.io

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Luke Zappia @lazappi.bsky.social · Apr 16

If they don't agree then it depends which you find more convincing I guess. I think there are lots of reasons two benchmarks might not after without either if them being "wrong" though.

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Luke Zappia @lazappi.bsky.social · Mar 20

Very on brand 😹. I guess I missed a space 🤦🏻. At least the mystery is solved.

Luke Zappia @lazappi.bsky.social · Mar 19

Yeah, it surprised me a bit as well. This wasn't the main aim of the paper though so it's a fairly limited comparison. There is a lot more you could do if you wanted to properly compare them.

Luke Zappia @lazappi.bsky.social · Mar 19

Thanks!

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Reposted by Luke Zappia

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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Luke Zappia @lazappi.bsky.social · Mar 19

Thanks!

Luke Zappia @lazappi.bsky.social · Mar 19

Thanks!

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Luke Zappia @lazappi.bsky.social · Mar 19

Hmmm...It's broken for me too 😿. I'm not sure what happened there but this is working www.nature.com/articles/s41.... Thanks for letting me know!

Feature selection methods affect the performance of scRNA-seq data integration and querying - Nature Methods

This Registered Report presents a benchmarking study evaluating the impact of feature selection on scRNA-seq integration.

www.nature.com

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Reposted by Luke Zappia

Philipp Bayer @philippbayer.bsky.social · Mar 17

We're hiring for a bioinformatics lead at the OceanOmics Centre! L7, come work with all of the cool genomics data!
HiFi, HiC, Illumina, a PromethION, it's all there. Sequence *all* of the marine vertebrates!

#bioinformatics

external.jobs.uwa.edu.au/cw/en/job/51...

Prospective staff : Jobs at UWA : IN DEVELOPMENT

external.jobs.uwa.edu.au

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Luke Zappia @lazappi.bsky.social · Mar 18

Big thank you to everyone who contributed to the study 🎉!

And thank you for reading 📖!

16/16

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Luke Zappia @lazappi.bsky.social · Mar 18

The project took 2.5 years from initial commit to publication. Some things could have been quicker but that’s not a complaint. I think that’s how long science takes and we should set realistic expectations, especially for junior researchers. It also emphasises the need for continuous benchmarking.

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Luke Zappia @lazappi.bsky.social · Mar 18

You can also find the code on GitHub github.com/theislab/atl... and the data on figshare figshare.com/projects/Ben....

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GitHub - theislab/atlas-feature-selection-benchmark: Code for "Feature selection methods affect the performance of scRNA-seq data integration and querying"

Code for "Feature selection methods affect the performance of scRNA-seq data integration and querying" - theislab/atlas-feature-selection-benchmark

github.com

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