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cole-trapnell-lab / cicero-release

https://cole-trapnell-lab.github.io/cicero-release/
MIT License
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Peak file for generating CDS #95

Closed rb56 closed 9 months ago

rb56 commented 11 months ago

Hello,

Im trying to run Cicero on scMultiome data (10x data) on 15 samples that have been integrated. I'm a little confused and unsure of the format of peaks file to make the Cell Data set object. In the tutorial (https://cole-trapnell-lab.github.io/cicero-release/docs_m3/) it mentions to use the matrix file however my dataset has aggregated data from 15 samples and Im not sure which input to use to generate the CDS.

Any help will be appreciated.

Thank you

hpliner commented 10 months ago

Hello, I'm not sure I have enough information to help, but I'd recommend taking a look at the monocle3 website for the various options for loading data here: https://cole-trapnell-lab.github.io/monocle3/docs/getting_started/#loading-data

However you end up with your cell data set object you should be able to continue with the cicero tutorial.