Data & ReproScientific VisualizationFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-workflows-crispr-screen-pipeline

Maintainer FreedomIntelligence · Last updated April 1, 2026

CRISPR screen: guide counting → MAGeCK → hit calling → visualization.

OpenClawNanoClawAnalysisWritingbio-workflows-crispr-screen-pipeline🧠 bioos extended suitebioos extended bioinformatics suitecrispr

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-workflows-crispr-screen-pipeline

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

mageck count \ -l library.csv \ -n experiment \ --sample-label Day0,Day14_Rep1,Day14_Rep2,Day14_Rep3 \ --fastq Day0.fastq.gz Day14_Rep1.fastq.gz Day14_Rep2.fastq.gz Day14_Rep3.fastq.gz \ --trim-5 0 \ --pdf-report.
def calculate_gini(x): x = np.sort(x[x > 0]) n = len(x) cumsum = np.cumsum(x) return (2 np.sum((np.arange(1, n+1) x)) - (n + 1) cumsum[-1]) / (n cumsum[-1]).

Source Doc

Excerpt From SKILL.md

Step 2: Quality Control

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

counts = pd.read_csv('experiment.count.txt', sep='\t', index_col=0)
counts_numeric = counts.iloc[:, 1:]

qc_stats = {}
for col in counts_numeric.columns:
    total = counts_numeric[col].sum()
    zeros = (counts_numeric[col] == 0).sum()
    gini = calculate_gini(counts_numeric[col].values)
    qc_stats[col] = {'total_reads': total, 'zero_count_guides': zeros, 'gini': gini}

qc_df = pd.DataFrame(qc_stats).T
print('QC Summary:')
print(qc_df)

## QC thresholds

assert qc_df['zero_count_guides'].max() < len(counts) * 0.2, 'Too many zero-count guides'
assert qc_df['gini'].max() < 0.4, 'Gini index too high (uneven distribution)'
print('QC passed!')

For dropout/negative selection screens

mageck test
-k experiment.count.txt
-t Day14_Rep1,Day14_Rep2,Day14_Rep3
-c Day0
-n negative_screen
--pdf-report
--gene-lfc-method alphamedian

Use cases

Use bio-workflows-crispr-screen-pipeline to prepare publication-quality figures.
Apply bio-workflows-crispr-screen-pipeline when results need clear visual communication.