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Fix linting
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cavenel committed Nov 29, 2023
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Expand Up @@ -112,21 +112,21 @@ The pipeline is using Python and the scverse tools to do the downstream analysis

The following parameters are exposed for preprocessing:

- `--st_preprocess_min_counts`: Minimum number of counts for a spot to be considered in the analysis.
- `--st_preprocess_min_genes`: Minimum number of genes expressed in a spot for the spot to be considered.
- `--st_preprocess_min_cells`: Minimum number of spots expressing a gene for the gene to be considered.
- `--st_preprocess_fig_size`: The figure size for the plots generated during preprocessing (e.g., quality control plots).
- `--st_preprocess_hist_qc_max_total_counts`: Maximum total counts for the histogram plot in quality control.
- `--st_preprocess_hist_qc_min_gene_counts`: Minimum gene counts for the histogram plot in quality control.
- `--st_preprocess_hist_qc_bins`: Number of bins for the histogram plot in quality control.
- `--st_preprocess_min_counts`: Minimum number of counts for a spot to be considered in the analysis.
- `--st_preprocess_min_genes`: Minimum number of genes expressed in a spot for the spot to be considered.
- `--st_preprocess_min_cells`: Minimum number of spots expressing a gene for the gene to be considered.
- `--st_preprocess_fig_size`: The figure size for the plots generated during preprocessing (e.g., quality control plots).
- `--st_preprocess_hist_qc_max_total_counts`: Maximum total counts for the histogram plot in quality control.
- `--st_preprocess_hist_qc_min_gene_counts`: Minimum gene counts for the histogram plot in quality control.
- `--st_preprocess_hist_qc_bins`: Number of bins for the histogram plot in quality control.

### Parameters for Clustering :

- `--st_cluster_resolution`: Resolution parameter for the clustering algorithm, controlling granularity.
- `--st_cluster_resolution`: Resolution parameter for the clustering algorithm, controlling granularity.

### Parameters for Spatial Differential Expression :

- `st_spatial_de_ncols`: Number of columns in the output figure.
- `st_spatial_de_ncols`: Number of columns in the output figure.

## Running the pipeline

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