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cole-trapnell-lab / cicero-release

https://cole-trapnell-lab.github.io/cicero-release/
MIT License
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make_atac_cds() does not generate cell_data_set object #94

Closed ivykos closed 11 months ago

ivykos commented 11 months ago

Good day

I am currently following the Cicero tutorial at https://cole-trapnell-lab.github.io/cicero-release/docs_m3/, and I am having an issue with converting my data to a cell_data_set object. I only have monocle3 and Cicero packages installed, but when I put my data into the make_atac_cds() function, it generated a CellDataSet object rather than a cell_data_set object, because when I try to use the detect_genes() function it returns the error Error: methods::is(object = cds, class2 = "cell_data_set") is not TRUE

ivykos commented 11 months ago

Update: problem was solved by installing the correct version of Garnett and restarting RStudio session (https://github.com/cole-trapnell-lab/monocle3/issues/372)