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OSCA-source / OSCA

The package wrapping the book, for deployment via the Bioconductor build system.
https://bioconductor.org/checkResults/devel/books-LATEST/OSCA
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Addition to demultiplexing chapter #7

Open huklein opened 1 year ago

huklein commented 1 year ago

Hello, I am the developer of demuxmix, a novel package for demultiplexing single-cell RNA sequencing data utilizing HTOs. I am curious if you would consider including it as an alternative to hashedDrops() in chapter 7.4.3 (under Advanced). The same example dataset from Stoeckius et al. could also be used for demuxmix, including a brief comparison of the demultiplexing results. I can assist with drafting the paragraph and providing sample code, if that helps.

demuxmix package: https://bioconductor.org/packages/release/bioc/html/demuxmix.html manuscript: https://www.biorxiv.org/content/10.1101/2023.01.27.525961v1 benchmark: https://www.biorxiv.org/content/10.1101/2022.12.20.521313v2

PeteHaitch commented 1 year ago

Hi @huklein,

I think that'd make a great addition! The repo with the relevant chapter is https://github.com/OSCA-source/OSCA.advanced, in particular https://github.com/OSCA-source/OSCA.advanced/blob/master/inst/book/droplet-processing.Rmd, and @geistlinger is the current maintainer of the relevant section of the book (OSCA.advanced). I'd be happy to help with incorporating it since I also reviewed the demuxmix submission to BioC but I'm on leave until April 25 and won't be able to provide any feedback until I'm back from leave.

Cheers, Pete