Comments (3)
Hi Laura,
Thanks for your interest!
Currently we did not plan for making a SCINA python implementation. As a workaround, would you like to try wrapping SCINA functions in a shell command, and call the command with python when in use? Please let me know if you have questions about wrapping up functions. Thanks!
Best regards, Ze
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from scina.
Hi Laura,
Would you please download the scripts in the R command folder (https://github.com/jcao89757/SCINA/tree/master/R) and try the linux wrapper EM_interface.R? Most of its parameters are the same as the SCINA package, and there is an example linux command in the script comments at the beginning of the code.
The linux command can then be called with python using the os package. The 'naive approach' using os.system in this workflow (https://www.section.io/engineering-education/how-to-execute-linux-commands-in-python/) will achieve the function. Please let me know if anything is not clear with the usage of the code and I'll be glad to help with any of your questions.
Have a nice weekend!
Best regards, Ze
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Related Issues (20)
- Conversion to dense matrix HOT 1
- SCINA error HOT 9
- SCINA error message HOT 12
- Signature vector where no cell markers match cell types causes an error HOT 2
- Is SCINA non-deterministic as an EM-framework? HOT 3
- Error when gene in signature list not present in expression matrix HOT 1
- Error Message in SCINA HOT 9
- Cannot annotate my own gene list with an error HOT 3
- Can't install the package using `install_github` HOT 1
- question about 'allow_unknown' parameter HOT 5
- signatures and plotheat.SCINA function
- License for GitHub and CRAN versions HOT 4
- annotat the aggregated cluster profile HOT 2
- cell type assignment with negative expression HOT 1
- Error with SCINA command HOT 16
- Addressing Heatmap Legend Overlap Issue in SCINA: Troubleshooting and Solutions HOT 1
- Error with SCINA command HOT 1
- possible bug in plotheat.SCINA? HOT 2
- function: plotheat.SCINA()
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