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AlexsLemonade / alsf-scpca

Management and analysis tools for ALSF Single-cell Pediatric Cancer Atlas data.
BSD 3-Clause "New" or "Revised" License
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Workflows for CITE-seq #50

Closed jashapiro closed 3 years ago

jashapiro commented 3 years ago

CITE-seq experiments will require additional processing to identify the cell surface markers that have been assayed.

This issue is vague for now, as I think we will want to see what the data we get looks like, but for reference, a few links that will be useful:

The CITE-seq website: https://cite-seq.com/computational-tools/

A tool for counting tags from the citeseq data: https://github.com/Hoohm/CITE-seq-Count

Orchestrating Single Cell on Protein Data: http://bioconductor.org/books/release/OSCA/integrating-with-protein-abundance.html

The CiteFuse package in R https://bioconductor.org/packages/release/bioc/html/CiteFuse.html

jashapiro commented 3 years ago

Meant to add this to the issue: Alevin-fry workflow for cite-seq: https://combine-lab.github.io/alevin-fry-tutorials/2021/af-feature-bc/

jashapiro commented 3 years ago

An initial workflow for CITE-seq mapping was completed in https://github.com/AlexsLemonade/alsf-scpca/pull/120

This is now being integrated into scpca-nf: https://github.com/AlexsLemonade/scpca-nf/pull/5

jashapiro commented 3 years ago

Since the mapping workflows are done, I am closing this in favor of some more explicit steps for finalizing the integration.