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[automated] Fix code linting
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docs/usage.md

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@@ -63,7 +63,7 @@ For CSV input files, specifying the `batch_col`, `label_col`, `condition_col`, a
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| `min_counts_cell` | Minimum number of counts required for a cell to be considered. Defaults to `1`. |
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| `min_counts_gene` | Minimum number of counts required for a gene to be considered. Defaults to `1`. |
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| `expected_cells` | Number of expected cells, used as input to CellBender for empty droplet detection. |
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| `doublet_rate` | Optional expected doublet rate (0-1) for `scDblFinder`. If not provided, `scDblFinder` estimates it internally. |
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| `doublet_rate` | Optional expected doublet rate (0-1) for `scDblFinder`. If not provided, `scDblFinder` estimates it internally. |
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| `max_mito_percentage` | Maximum percentage of mitochondrial reads for a cell to be considered. Defaults to `100`. |
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| `ambient_correction` | Whether to perform ambient RNA correction for this sample. Set to `true` to use the globally configured method, `false` to skip ambient correction for this sample. Defaults to `true`. |
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| `ambient_corrected_integration` | Whether to use ambient-corrected counts for integration for this sample. Set to `true` to use corrected counts in downstream integration, `false` to store them only as additional layers. Can override the global `--ambient_corrected_integration` parameter. Defaults to global setting. |

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