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fix linting error
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shiltemann committed Feb 27, 2025
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Expand Up @@ -194,12 +194,12 @@ The first step is to import the datasets into an AnnData object using the *pp.im
The {TSSe} threshold balances data retention and quality control. In our dataset, the {TSSe} distributions indicate substantial differences in sample quality between batches. To retain as much biological data as possible, we will use a broader filter (e.g., minimum {TSSe} = 7.0).
**Standard {TSSe} Thresholds**
Standard {TSSe} Thresholds
- **Strict (TSSe ≥ 10–15)**: High-confidence cells.
- **Moderate (TSSe ≥ 7–10)**: Balances data retention and quality but may include lower-quality cells.
- **Broad (TSSe ≥ 5–7)**: Maximizes retention but increases the risk of including lower-quality data.
**Choosing the Right Cutoff**
Choosing the Right Cutoff
- If sample quality varies, a **moderate threshold (≥7.0)** helps retain more data.
- If high-quality data is required, **stricter filtering (≥10.0)** is recommended.
- Inspect {TSSe} distributions to determine the most suitable threshold for your dataset.
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