Feature/filtering qc metrics highly variable genes#8
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…election - Added filter_data() to filter out low-quality cells and genes - Added calculate_qc_metrics() to compute mitochondrial gene percentages and other QC stats - Added select_highly_variable_genes() to identify informative genes for downstream analysis These reusable functions improve code clarity and support scalable single-cell preprocessing workflows.
TRextabat
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Apr 9, 2025
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that is great work Thx @Oykupnrbs @Ekin-hub-code
TRextabat
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Apr 9, 2025
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| def calculate_qc_metrics(adata: AnnData) -> AnnData: | ||
| """ | ||
| Computes quality control (QC) metrics and adds them to the dataset. | ||
| Checks for mitochondrial genes with both uppercase and lowercase 'mt-' prefix. | ||
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| Args: | ||
| adata (AnnData): The filtered dataset. | ||
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| Returns: | ||
| AnnData: Dataset with QC metrics added. | ||
| """ | ||
| if adata.var_names.str.startswith("MT-").any(): | ||
| adata.var["mt"] = adata.var_names.str.startswith("MT-") | ||
| elif adata.var_names.str.startswith("mt-").any(): | ||
| adata.var["mt"] = adata.var_names.str.startswith("mt-") | ||
| else: | ||
| # In case neither is found, check in a case-insensitive way just to be sure | ||
| adata.var["mt"] = adata.var_names.str.upper().str.startswith("MT-") | ||
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| sc.pp.calculate_qc_metrics( | ||
| adata, | ||
| qc_vars=["mt"], | ||
| percent_top=None, | ||
| log1p=False, | ||
| inplace=True | ||
| ) |
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you could add mt and MT as argument in future maybe we want to avoid mt filtration
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Pull Request Description:
This pull request adds three simple and reusable functions for preprocessing single-cell RNA-seq data with Scanpy.
What’s inside:
filter_data():Removes cells with too few genes, and genes found in too few cells.calculate_qc_metrics():Finds mitochondrial genes and calculates quality control values.select_highly_variable_genes():Picks genes that are most variable for further analysis.Demo Code:
Creates random fake data to test the functions.
Adds example mitochondrial genes to test QC.
Runs all three functions step by step with print statements to see results.
Why this is useful:
Code is now easier to read and use in other projects.
The demo shows how everything works in a simple way.
Demo Output:
