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Dear cellphonedb team,
thanks for providing and maintaining such a great resource. In one of the analysis I performed with cellphonedb the following interaction came up:
HLADPB1 - NRG1
I found …
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Points to be discussed
- images:
- features?
- spatial graph:
- Integrate cellphoneDb/omnipath to neighborhood enrichment to provide ligand receptor pair in a straighforward way (Giovanni)
…
giovp updated
3 years ago
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Hello,
I am having issues when attempting the function ```create_domino```.
When I run the function, I get the following error:
```
> pbmc_dom = create_domino(signaling_db = '/Users/melanie/…
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Hi,
I'm new to single-cell RNA seq and was wondering if anyone could explain a bit more about the basics of using CellphoneDB,
the instructions seem to be good for the terminal? But how might one …
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I have tried both "cellphonedb method statistical_analysis" and "cellphonedb method analysis" (normal mode). Couple questions:
1. Compared with statistical_analysis, the normal mode does not perform …
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Hi. I get the same error message when I try to run the dotplot or heatmap functions. As a consequence, I can't find the plot neither in the output directory nor anywhere else. Even though the plot pop…
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Hi!
I am trying to install CellPhoneDB in a singularity image based on ubutu.
You standard pip install cellphonedb does fail with a compile error in the
'Building wheels for collected packages: p…
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Hi,
When I ran CellPhoneDB on my scRNA data, I got the following error messages on some samples.
[ ][APP][10/09/20-22:19:17][ERROR] Unexpected error
/nas/longleaf/apps/python/3.6.6/lib/python3.6/…
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Hi, thanks for the great tool!
would it be possible to accept large matrices in the mtx format instead of txt? or did you think of a fast routine to convert sparse matrices to an input that the tool …
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I encountered this error when running cellphoneDB on the Decidua dataset. The command is as below:
cellphonedb method statistical_analysis meta_10x.txt raw_data_10x.txt
The set column names se…