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Added data format advice for user's input files - based on recent Git…
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datasome committed Oct 31, 2023
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Expand Up @@ -203,6 +203,14 @@ score_interactions = True
> Important: to calculate the score, all the cells present in the dataset are employed (steps 1-4). If microenvironmens are defined, the score (step) 5 will be calculated only for cells within the same microenvironment.
# Input files
## Data format advice
NOTE Please _do not use_ the following in any of your input (e.g. Counts and Meta) files:
> Numeric cell type names (see [GitHub issue #148](https://github.com/ventolab/CellphoneDB/issues/148))
> Dashes ("-") in cell names (see [GitHub issue #144](https://github.com/ventolab/CellphoneDB/issues/144)))
## Counts file
For large datasets, do not use .txt files to input counts `test_counts.txt`. Please, input counts as h5ad (recommended), h5 or a path to a folder containing a 10x output with mtx/barcode/features files.
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