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cole-trapnell-lab / cicero-release

https://cole-trapnell-lab.github.io/cicero-release/
MIT License
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Question for trajector analysis #46

Closed crushseven-7 closed 4 years ago

crushseven-7 commented 4 years ago

Hi, Thank you for your wonderful software. Currently I am working on scATAC-seq data trajectory analysis. After I prepared input_cds and run estimate_size_factors() function, I got this error: Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'counts' for signature '"CellDataSet"' How shall I modify the input cds to avoid this error?

Thank you, Best, Yan

hpliner commented 4 years ago

Hi Yan,

This error occurs when you're mixing monocle and monocle3. You have to make sure you have either monocle3 and cicero for monocle3 (see here) or monocle and cicero for monocle (see here)

Hope this helps

crushseven-7 commented 4 years ago

Thank you for your helpful info. Last time I install cicero in coda with command conda install -c bioconda bioconductor-cicero . In retrospect, this cicero is for monocle.