The Spatial Transcriptomics Toolkit: Memory, Clustering, and Deconvolution

18min | 09/02/2025

Description

In this episode, Alex and Lorena tackle the computational challenges of spatial transcriptomics. Learn how BPCells can help you work with millions of cells without needing terabytes of RAM, discover how Banksy's neighborhood-aware clustering reveals tissue architecture, and explore RCTD's approach to cell type deconvolution in spatially-resolved data. Plus, Lorena reviews Positron, the new R-friendly IDE that's catching attention in the bioinformatics community.

https://github.com/bnprks/BPCells

https://github.com/prabhakarlab/Banksy

https://github.com/dmcable/spacexr

https://github.com/bcbio/spatial-reports

https://github.com/seandavi/awesome-single-cell

https://positron.posit.co/

Send us your comments, questions, and suggestions using this form 📁: https://forms.gle/ncwo6HZeN4uA9gPg7

Follow us on LinkedIn: https://www.linkedin.com/in/lpantano/ and https://www.linkedin.com/in/alexandra-bartlett-926b32109/

Thanks to Amulya Shastry for editing and management support.

If you enjoyed the episode, please subscribe and leave us a review. Subscribe here: https://podcast.ausha.co/a-coffee-with-compbio?s=1

Hosted on Ausha. See ausha.co/privacy-policy for more information.

About A Coffee with CompBio

Step into the world where algorithms meet biology! Hosts Lorena Pantano and Alex Bartlett, two dynamic women in science, unravel the complexities and curiosities of computational biology. Each episode, they break down complicated analyses, demystify big data approaches, and share real-world stories from their own bioinformatics research adventures. Whether you’re a seasoned bioinformatician or just bio-curious, Alex and Lorena's engaging banter, expert interviews, and practical tips will guide you through the fascinating process of turning raw biological data into meaningful scientific discoveries. Join them as they make computation in the life sciences accessible—and even a little bit fun!

Hosted on Ausha. See ausha.co/privacy-policy for more information.

About A Coffee with CompBio

Step into the world where algorithms meet biology! Hosts Lorena Pantano and Alex Bartlett, two dynamic women in science, unravel the complexities and curiosities of computational biology. Each episode, they break down complicated analyses, demystify big data approaches, and share real-world stories from their own bioinformatics research adventures. Whether you’re a seasoned bioinformatician or just bio-curious, Alex and Lorena's engaging banter, expert interviews, and practical tips will guide you through the fascinating process of turning raw biological data into meaningful scientific discoveries. Join them as they make computation in the life sciences accessible—and even a little bit fun!

Hosted on Ausha. See ausha.co/privacy-policy for more information.

Description

In this episode, Alex and Lorena tackle the computational challenges of spatial transcriptomics. Learn how BPCells can help you work with millions of cells without needing terabytes of RAM, discover how Banksy's neighborhood-aware clustering reveals tissue architecture, and explore RCTD's approach to cell type deconvolution in spatially-resolved data. Plus, Lorena reviews Positron, the new R-friendly IDE that's catching attention in the bioinformatics community.

https://github.com/bnprks/BPCells

https://github.com/prabhakarlab/Banksy

https://github.com/dmcable/spacexr

https://github.com/bcbio/spatial-reports

https://github.com/seandavi/awesome-single-cell

https://positron.posit.co/

Send us your comments, questions, and suggestions using this form 📁: https://forms.gle/ncwo6HZeN4uA9gPg7

Follow us on LinkedIn: https://www.linkedin.com/in/lpantano/ and https://www.linkedin.com/in/alexandra-bartlett-926b32109/

Thanks to Amulya Shastry for editing and management support.

If you enjoyed the episode, please subscribe and leave us a review. Subscribe here: https://podcast.ausha.co/a-coffee-with-compbio?s=1

Hosted on Ausha. See ausha.co/privacy-policy for more information.

About A Coffee with CompBio

Step into the world where algorithms meet biology! Hosts Lorena Pantano and Alex Bartlett, two dynamic women in science, unravel the complexities and curiosities of computational biology. Each episode, they break down complicated analyses, demystify big data approaches, and share real-world stories from their own bioinformatics research adventures. Whether you’re a seasoned bioinformatician or just bio-curious, Alex and Lorena's engaging banter, expert interviews, and practical tips will guide you through the fascinating process of turning raw biological data into meaningful scientific discoveries. Join them as they make computation in the life sciences accessible—and even a little bit fun!

Hosted on Ausha. See ausha.co/privacy-policy for more information.

About A Coffee with CompBio

Step into the world where algorithms meet biology! Hosts Lorena Pantano and Alex Bartlett, two dynamic women in science, unravel the complexities and curiosities of computational biology. Each episode, they break down complicated analyses, demystify big data approaches, and share real-world stories from their own bioinformatics research adventures. Whether you’re a seasoned bioinformatician or just bio-curious, Alex and Lorena's engaging banter, expert interviews, and practical tips will guide you through the fascinating process of turning raw biological data into meaningful scientific discoveries. Join them as they make computation in the life sciences accessible—and even a little bit fun!

Hosted on Ausha. See ausha.co/privacy-policy for more information.

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