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Mayrlab / scUTRquant

Bioinformatics pipeline for single-cell 3' UTR isoform quantification
https://Mayrlab.github.io/scUTRquant
GNU General Public License v3.0
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using scUTRboot to calculate LUI #60

Open rhea9184 opened 1 year ago

rhea9184 commented 1 year ago

Hi,

I have some scRNAseq data that I ran through the scUTRquant pipeline and would like to now calculate the LUI for the transcripts. Is there a pipeline or some code from the authors I might be able to use?

Thank you so much for your help!

mfansler commented 1 year ago

Hi @rhea9184, thanks for the interest!

We don't have a tutorial or pipeline for this downstream analysis yet. However, all the code used to generate the Figures for the manuscript can be found in the scUTRquant-figures repository. Figures 2 (LUI point estimates for batches), 4 (analysis of mouse data), and 5 (analysis when using custom txcutr annotations) would be the most relevant. Note that the knitted branch includes rendered HTML versions.

There is an example of using scUTRboot to do statistical testing of two clusters in the Fig. 4c file, including both LUI tests and the WD tests. For estimating LUIs, without testing, there is code in the Fig. 4ab file that performs bootstrap estimates.

Please don't hesitate to ask for any clarifications/help. I'm planning to add functionality and examples to scUTRboot in the coming weeks, so feedback is welcome!