bio-crispr-screens-screen-qc

Load Count Data

import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns

## Library Representation

**Goal:** Assess whether the sgRNA library is adequately represented across all samples.

**Approach:** Count zero-count and low-count sgRNAs per sample, flagging samples where dropout exceeds quality thresholds (>1% zero-count is warning, >5% is failure).

```python

## Zero-count sgRNAs per sample

zero_counts = (count_matrix == 0).sum()
zero_pct = zero_counts / len(count_matrix) * 100

print('Zero-count sgRNAs per sample:')
for sample, pct in zero_pct.items():
    status = 'OK' if pct < 1 else 'WARNING' if pct < 5 else 'FAIL'
    print(f'  {sample}: {pct:.2f}% [{status}]')