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Teichlab / tracer

TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data
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TraCeR integration with R-based tools #106

Closed andresnoe closed 3 years ago

andresnoe commented 3 years ago

Hi Mike,

Thanks for your work on TraCeR. I've just run it on my SmartSeq2 data set and am wondering if there are any straightforward methods for integration with R-based tools/workflows? I'm thinking something similar to scRepertoire's ability to take filtered contig outputs from 10x Cell Ranger (or similarly, ImmunArch (used to be called tcR)). I've been looking for a few days now and can't find anything that seems to pull in the TraCeR output simply. Ideally, I'd want something that allows me to do clonotype-only analysis functions (eg. unique clonotypes) and look at interaction with mRNA expression data using Seurat or SingleCellExperiment objects. Open to broad brush stroke ideas.

Warm regards,

Andrés

andresnoe commented 3 years ago

Ah... forgot to mention the main inspiration for this post. I saw this pre-print for scirpy, single-cell T-cell receptor sequencing data analysis tool. Is there any similar R equivalent?

mstubb commented 3 years ago

Hi Andrés,

Unfortunately, I don't know of any R-based tools that parse TraCeR output. Sorry.

If you were willing to work in Python then I think scirpy could help with what you want but I don't have any direct experience with it.

Very best,

Mike