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CHOIR is now online Nature Genetics! CHOIR is a new clustering method for single-cell data that evaluates whether clusters represent statistically distinct cell populations. CHOIR scales to millions of cells and works with single-/multi-omic data of any type!

Cathrine Sant

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55,296 views • 1 year ago •via X (Twitter)

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Cathrine Sant (Petersen)1 year ago

CHOIR is available as a user-friendly R package, compatible with Seurat, SingleCellExperiment, and ArchR input objects. We’ve compiled detailed documentation & tutorials on our website:

Cathrine Sant (Petersen)1 year ago

We received great input during the review process, which led us to improve the tool in multiple ways. Single-cell datasets are getting larger by the day, and CHOIR is now compatible with atlas-scale data—as shown here on >3M cells from a human brain atlas snRNA-seq dataset!

Cathrine Sant (Petersen)1 year ago

We’ve also made CHOIR compatible with count splitting ( wherein two independent matrices are used avoid the problem of “double dipping” wherein the same data is used to both generate and evaluate clusters.

Cathrine Sant (Petersen)1 year ago

So thankful for the support of my PhD advisors Lennart Mucke & Ryan Corces @doctorcorces, as well as all of the people who have used CHOIR and provided input! Check out our GitHub page for the latest updates & to report issues—feedback is always welcome!

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Alessandro Crimi 🧠🧬🔬🩺( @alecrimi.bsky.social )1 year ago

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New preprint! So excited to present CHOIR, a new clustering method for single-cell data that evaluates whether clusters represent statistically distinct cell populations. CHOIR works with both single- and multi-omic data of any type. Check it out!

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