qc_analysis

Performs comprehensive quality control on single-cell RNA-seq data, including calculating metrics, generating QC plots, and filtering cells.

Skills
Scientific
1

What it does and how to use it

A skill that teaches Claude Code to do scientific tasks well. It is packaged knowledge the model uses whenever it is relevant.

Install the skill (command above).
In Claude Code, describe what you need - the skill turns on by itself when the context fits.
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Install (Claude Code)

mkdir -p .claude/skills/qc-analysis && curl -fsSL https://doutorai.pt/data/lib/skills__qc-analysis.md -o .claude/skills/qc-analysis/SKILL.md

Paste this command into the terminal, in your project folder, and the component installs automatically.

Content

#!/usr/bin/env python3
"""
Quality Control Analysis Script for Scanpy

Performs comprehensive quality control on single-cell RNA-seq data,
including calculating metrics, generating QC plots, and filtering cells.

Usage:
    python qc_analysis.py <input_file> [--output <output_file>]
"""

import argparse
import scanpy as sc
import matplotlib.pyplot as plt


def calculate_qc_metrics(adata, mt_threshold=5, min_genes=200, min_cells=3):
    """
    Calculate QC metrics and filter cells/genes.

    Parameters:
    -----------
    adata : AnnData
        Annotated data matrix
    mt_threshold : float

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