search

digitalcytometry / ecotyper

EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
Other
177 stars 41 forks source link

Running bulk recovery with published cell states #94

Closed WJRDW closed 2 months ago

WJRDW commented 3 months ago

Hi!

Thank you very much for building this amazing tool! I'm interested in recovering cell states and ecotypes from bulk RNA sequencing data using published cell states in sarcomas (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11058033/). The cell state markers of the different identified cell states are publicly available in the supplementary information of the article in an excel file. cell state markers I succesfully installed all components needed to run the bulk recovery analysis and can run the examples. My question is how I should structure the published cell states (should the markers for each cell type be in a separate .txt file and seperate folder?) and how to feed it into the algorithm. Thank you very much for your help!

cbsteen commented 2 months ago

Thank you for your interest in EcoTyper. I would recommend to follow the instructions provided by the authors.