Luke Zappia
@lazappi.bsky.social
Bioinformatician, data scientist, software developer
Also @_lazappi_ and @lazappi@mastodon.au
Also @_lazappi_ and @lazappi@mastodon.au
Reposted by Luke Zappia
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
Ie: it's not us (Samtools team)! Be warned
September 15, 2025 at 8:40 AM
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
Ie: it's not us (Samtools team)! Be warned
Reposted by Luke Zappia
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...
August 29, 2025 at 10:15 AM
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...
Reposted by Luke Zappia
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
August 25, 2025 at 3:24 PM
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
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.
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.
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
🔗 Read the paper: www.biorxiv.org/content/10.1...
💻 Check the package in action: anndatar.data-intuitive.com
August 26, 2025 at 5:36 AM
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.
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.
Reposted by Luke Zappia
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
🔗 Read the paper: www.biorxiv.org/content/10.1...
💻 Check the package in action: anndatar.data-intuitive.com
August 25, 2025 at 3:24 PM
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
🔗 Read the paper: www.biorxiv.org/content/10.1...
💻 Check the package in action: anndatar.data-intuitive.com
Reposted by Luke Zappia
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? 🧪
What advice do you have to share with my students? 🧪
June 17, 2025 at 3:10 PM
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? 🧪
What advice do you have to share with my students? 🧪
Reposted by Luke Zappia
[Bioc-devel] Bioconductor is moving from Slack to Zulip – 2 June
stat.ethz.ch
May 30, 2025 at 10:19 PM
Reposted by Luke Zappia
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
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
May 13, 2025 at 11:44 PM
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
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
Reposted by Luke Zappia
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🧵
June 3, 2025 at 8:24 AM
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🧵
Reposted by Luke Zappia
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...
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...
May 27, 2025 at 4:59 AM
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...
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...
Reposted by Luke Zappia
🔥 Just published! Thrilled to share that our work on funkyheatmap has just been published in the Journal of Open Source Software 🎉
May 1, 2025 at 2:20 PM
🔥 Just published! Thrilled to share that our work on funkyheatmap has just been published in the Journal of Open Source Software 🎉
Reposted by Luke Zappia
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
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
April 28, 2025 at 5:13 AM
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
Their tips and tricks are collected in this blog: hrovatin.github.io/posts/r_pyth...
@lazappi.bsky.social @t-kalinowski.bsky.social
Reposted by Luke Zappia
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
Keep reading for more about how we did the study and what we found out 🧵 👇
1/16
https://www.nature.com/articles/s41592-025-02624-3🎉
March 18, 2025 at 3:40 PM
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
Keep reading for more about how we did the study and what we found out 🧵 👇
1/16
Reposted by Luke Zappia
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...
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
March 17, 2025 at 7:02 AM
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...
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...
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
Keep reading for more about how we did the study and what we found out 🧵 👇
1/16
https://www.nature.com/articles/s41592-025-02624-3🎉
March 18, 2025 at 3:40 PM
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
Keep reading for more about how we did the study and what we found out 🧵 👇
1/16
Reposted by Luke Zappia
🚨🧠 New paper alert: Stress alters neuronal balance in the developing brain 🧠🚨
Our latest study in @science.orgAdvances explores how glucocorticoid exposure—a key environmental risk factor—shapes early human brain development using #organoids.
@mpi-psychiatry.bsky.social @drcricru.bsky.social
🧵👇
Our latest study in @science.orgAdvances explores how glucocorticoid exposure—a key environmental risk factor—shapes early human brain development using #organoids.
@mpi-psychiatry.bsky.social @drcricru.bsky.social
🧵👇
Chronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids
Chronic exposure to glucocorticoids during brain development leads to priming of the inhibitory neuron lineages in organoids.
www.science.org
February 21, 2025 at 10:14 AM
🚨🧠 New paper alert: Stress alters neuronal balance in the developing brain 🧠🚨
Our latest study in @science.orgAdvances explores how glucocorticoid exposure—a key environmental risk factor—shapes early human brain development using #organoids.
@mpi-psychiatry.bsky.social @drcricru.bsky.social
🧵👇
Our latest study in @science.orgAdvances explores how glucocorticoid exposure—a key environmental risk factor—shapes early human brain development using #organoids.
@mpi-psychiatry.bsky.social @drcricru.bsky.social
🧵👇
Do any #rstats reticulate experts have examples of using register_module_help_handler() or register_help_topics()? I feel like these should be able to let a package provide access to help information but there isn't much documentation on how to use them.
February 13, 2025 at 12:40 PM
Do any #rstats reticulate experts have examples of using register_module_help_handler() or register_help_topics()? I feel like these should be able to let a package provide access to help information but there isn't much documentation on how to use them.
Reposted by Luke Zappia
Thought for computational biologists choosing projects:
If you’re interested in method development, one counterintuitive strategy can be to dive deep into biology.
If you’re interested in method development, one counterintuitive strategy can be to dive deep into biology.
February 12, 2025 at 9:34 AM
Thought for computational biologists choosing projects:
If you’re interested in method development, one counterintuitive strategy can be to dive deep into biology.
If you’re interested in method development, one counterintuitive strategy can be to dive deep into biology.
Reposted by Luke Zappia
I just uploaded the first version of {{exactplot}} to github.com/const-ae/exa... 🎉
It produces figures with consistent font size, Latex labels, and millimeter-perfect layouting. It's an alternative to patchwork with less elegant syntax but much more flexibility.
#rstats
It produces figures with consistent font size, Latex labels, and millimeter-perfect layouting. It's an alternative to patchwork with less elegant syntax but much more flexibility.
#rstats
February 12, 2025 at 11:40 AM
I just uploaded the first version of {{exactplot}} to github.com/const-ae/exa... 🎉
It produces figures with consistent font size, Latex labels, and millimeter-perfect layouting. It's an alternative to patchwork with less elegant syntax but much more flexibility.
#rstats
It produces figures with consistent font size, Latex labels, and millimeter-perfect layouting. It's an alternative to patchwork with less elegant syntax but much more flexibility.
#rstats
Reposted by Luke Zappia
Check out our speakers for #ozsinglecell25.
May 21-23, Sydney
Registrations opening soon www.ozsinglecell.com
May 21-23, Sydney
Registrations opening soon www.ozsinglecell.com
January 30, 2025 at 6:38 AM
Check out our speakers for #ozsinglecell25.
May 21-23, Sydney
Registrations opening soon www.ozsinglecell.com
May 21-23, Sydney
Registrations opening soon www.ozsinglecell.com
Reposted by Luke Zappia
I am Stoked about our upcoming @scverse.bsky.social
and @owkin.bsky.social hackathon, focused on spatial omics data analysis.
📅 March 17-19, 2025
📍 Owkin office, Paris
Apply now: docs.google.com/forms/d/e/1F...
and @owkin.bsky.social hackathon, focused on spatial omics data analysis.
📅 March 17-19, 2025
📍 Owkin office, Paris
Apply now: docs.google.com/forms/d/e/1F...
Scverse x Owkin Hackathon in Paris
We're pleased to announce the next Scverse Hackathon will take place in the Owkin offices in Paris from 17/03/2025 9am to 19/03/2025 1:30pm.
This hackathon is a joint initiative between the scverse c...
docs.google.com
January 17, 2025 at 10:34 AM
I am Stoked about our upcoming @scverse.bsky.social
and @owkin.bsky.social hackathon, focused on spatial omics data analysis.
📅 March 17-19, 2025
📍 Owkin office, Paris
Apply now: docs.google.com/forms/d/e/1F...
and @owkin.bsky.social hackathon, focused on spatial omics data analysis.
📅 March 17-19, 2025
📍 Owkin office, Paris
Apply now: docs.google.com/forms/d/e/1F...
Reposted by Luke Zappia
Our paper on nurturing a #PositiveResearchCulture within your #research #team published by @wellcometrust.bsky.social gives useful tips for your lab. As well as making you a good team leader, nurturing culture pays off in building your science: 1/11
wellcomeopenresearch.org/articles/9-3...
wellcomeopenresearch.org/articles/9-3...
wellcomeopenresearch.org
January 14, 2025 at 9:55 AM
Our paper on nurturing a #PositiveResearchCulture within your #research #team published by @wellcometrust.bsky.social gives useful tips for your lab. As well as making you a good team leader, nurturing culture pays off in building your science: 1/11
wellcomeopenresearch.org/articles/9-3...
wellcomeopenresearch.org/articles/9-3...
Reposted by Luke Zappia
We are here 🦋. Save the date for Oz Single Cell 2025, 23-25 May in Sydney
January 7, 2025 at 3:49 AM
We are here 🦋. Save the date for Oz Single Cell 2025, 23-25 May in Sydney
Reposted by Luke Zappia
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.
December 15, 2024 at 10:51 PM
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.
Reposted by Luke Zappia
1/7 Planning to build a single-cell atlas? Or wondering how atlases can be useful to your research? Read our guide on single-cell atlases www.nature.com/articles/s41... published in Nature Methods, by @lisasikkema.bsky.social, @khrovatin.bsky.social, Malte Luecken, @fabiantheis.bsky.social et al.
December 13, 2024 at 10:33 AM
1/7 Planning to build a single-cell atlas? Or wondering how atlases can be useful to your research? Read our guide on single-cell atlases www.nature.com/articles/s41... published in Nature Methods, by @lisasikkema.bsky.social, @khrovatin.bsky.social, Malte Luecken, @fabiantheis.bsky.social et al.