Can Ergen
@canergen.bsky.social
single-cell genomics, spatial transcriptomics, T cell immunology, IBD
Reposted by Can Ergen
Extremely proud of @justjhong.bsky.social @khushipde.bsky.social for bringing this innovation to life! #AMICI🤝 redefines #attention for cell–cell interaction inference from #spatial #transcriptomics going beyond proximity to capture who talks to whom, at what distance and w/ what downstream impact!
September 25, 2025 at 1:39 PM
Extremely proud of @justjhong.bsky.social @khushipde.bsky.social for bringing this innovation to life! #AMICI🤝 redefines #attention for cell–cell interaction inference from #spatial #transcriptomics going beyond proximity to capture who talks to whom, at what distance and w/ what downstream impact!
Reposted by Can Ergen
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 Can Ergen
scverse turns 3!
What started as a shared vision for interoperable single-cell analysis has become a vibrant, global community.
From AnnData to full multimodal pipelines, we’re building the future of everything single-cell and spatial omics, together.
Here’s to what’s next!
What started as a shared vision for interoperable single-cell analysis has become a vibrant, global community.
From AnnData to full multimodal pipelines, we’re building the future of everything single-cell and spatial omics, together.
Here’s to what’s next!
May 17, 2025 at 10:08 PM
scverse turns 3!
What started as a shared vision for interoperable single-cell analysis has become a vibrant, global community.
From AnnData to full multimodal pipelines, we’re building the future of everything single-cell and spatial omics, together.
Here’s to what’s next!
What started as a shared vision for interoperable single-cell analysis has become a vibrant, global community.
From AnnData to full multimodal pipelines, we’re building the future of everything single-cell and spatial omics, together.
Here’s to what’s next!
Reposted by Can Ergen
We identify evidence of off-target probe binding in the 10x Genomics #Xenium v1 Human Breast Gene Expression Panel, compromising the accuracy of resulting #singlecell #spatialtranscriptomics profiles
See our preprint for more details: www.biorxiv.org/content/10.1...
#AcademicSky
🧵👇 1/n
See our preprint for more details: www.biorxiv.org/content/10.1...
#AcademicSky
🧵👇 1/n
Evidence of off-target probe binding in the 10x Genomics Xenium v1 Human Breast Gene Expression Panel compromises accuracy of spatial transcriptomic profiling
The accuracy of spatial gene expression profiles generated by probe-based in situ spatially-resolved transcriptomic technologies depends on the specificity with which probes bind to their intended tar...
www.biorxiv.org
April 3, 2025 at 3:35 PM
We identify evidence of off-target probe binding in the 10x Genomics #Xenium v1 Human Breast Gene Expression Panel, compromising the accuracy of resulting #singlecell #spatialtranscriptomics profiles
See our preprint for more details: www.biorxiv.org/content/10.1...
#AcademicSky
🧵👇 1/n
See our preprint for more details: www.biorxiv.org/content/10.1...
#AcademicSky
🧵👇 1/n
Reposted by Can Ergen
A pre-trained SCVI model of our Tahoe-100M cell atlas is now available as a HubModel! It can be used for gene expression visualization, differential expression, or cell clustering. Available at Hugging Face with instructions on how to load it (see thread)
March 6, 2025 at 11:01 PM
A pre-trained SCVI model of our Tahoe-100M cell atlas is now available as a HubModel! It can be used for gene expression visualization, differential expression, or cell clustering. Available at Hugging Face with instructions on how to load it (see thread)
Reposted by Can Ergen
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 Can Ergen
I was just looking at our @scverse.bsky.social zulip chat statistics and am super happy about our steady and healthy growth. The two bursts are our official launch in May 2022 and the inaugural scverse conference in September of 2024. Please join us! scverse.zulipchat.com
December 15, 2024 at 3:52 PM
I was just looking at our @scverse.bsky.social zulip chat statistics and am super happy about our steady and healthy growth. The two bursts are our official launch in May 2022 and the inaugural scverse conference in September of 2024. Please join us! scverse.zulipchat.com
Reposted by Can Ergen
Wanted to learn more about VisiumHD barcodes to help build better tools for processing that exciting data
I asked 10x about parsing the binary spatial information file, they said:
"...the Visium HD barcodes...are proprietary..."
C'mon 10x. You're shooting yourselves (and users) in the foot here!
I asked 10x about parsing the binary spatial information file, they said:
"...the Visium HD barcodes...are proprietary..."
C'mon 10x. You're shooting yourselves (and users) in the foot here!
November 26, 2024 at 12:29 AM
Wanted to learn more about VisiumHD barcodes to help build better tools for processing that exciting data
I asked 10x about parsing the binary spatial information file, they said:
"...the Visium HD barcodes...are proprietary..."
C'mon 10x. You're shooting yourselves (and users) in the foot here!
I asked 10x about parsing the binary spatial information file, they said:
"...the Visium HD barcodes...are proprietary..."
C'mon 10x. You're shooting yourselves (and users) in the foot here!
Reposted by Can Ergen
Explore the scverse Starter Pack!
Stay informed about the latest scverse events, software updates, and community news. Everything you need to know about foundational tools for single-cell omics analysis in one place.
go.bsky.app/UvFMa8d
Stay informed about the latest scverse events, software updates, and community news. Everything you need to know about foundational tools for single-cell omics analysis in one place.
go.bsky.app/UvFMa8d
November 16, 2024 at 1:59 PM
Explore the scverse Starter Pack!
Stay informed about the latest scverse events, software updates, and community news. Everything you need to know about foundational tools for single-cell omics analysis in one place.
go.bsky.app/UvFMa8d
Stay informed about the latest scverse events, software updates, and community news. Everything you need to know about foundational tools for single-cell omics analysis in one place.
go.bsky.app/UvFMa8d