Perturbio

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│         Crop-Seq Analysis Made Simple                          │
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Perturbio is a comprehensive Python package for end-to-end analysis of Crop-Seq experiments (CRISPR pooled screens + single-cell RNA sequencing). From raw data to biological insights in under 5 minutes.

Features

• Guide Extraction: Automatically identify CRISPR guide RNAs in single cells
• Differential Expression: Discover genes affected by perturbations
• Beautiful Visualizations: Publication-ready plots with minimal code
• Scanpy Integration: Works seamlessly with the scanpy ecosystem
• Simple CLI: One command to run complete analysis
• Fast: Analyze thousands of cells in minutes

Installation

Install from source:

git clone https://github.com/Siavashghaffari/Perturbio.git
cd Perturbio
pip install -e .

Once released on PyPI:

pip install perturbio

Quick Start

Command Line

# Run complete analysis
perturbio analyze cropseq_data.h5ad --guides guides.csv

# Results saved to perturbio_results_YYYYMMDD_HHMMSS/

Python API

from perturbio import CropSeqAnalyzer

# One-liner magic
analyzer = CropSeqAnalyzer("cropseq_data.h5ad")
results = analyzer.run()

# Access results
print(results.top_hits("BRCA1_guide1", n=20))
results.plot_volcano("MYC_guide1")

Scanpy Integration

import scanpy as sc
import perturbio as pt

# Standard scanpy workflow
adata = sc.read_h5ad("cropseq_data.h5ad")
sc.pp.normalize_total(adata)
sc.pp.log1p(adata)

# Extract guides
pt.guides.extract(adata, guide_file="guides.csv")

# Differential expression
pt.tl.differential_expression(adata, groupby='perturbation', control='non-targeting')

# Visualize
pt.pl.volcano(adata, perturbation='BRCA1_guide1')

Guide Library Format

Create a CSV file with your guide library:

guide_id,target_gene,guide_sequence
BRCA1_guide1,BRCA1,GCACTCAGGAAACAGCTATG
BRCA1_guide2,BRCA1,CTGAAGACTGCTCAGTGTAG
MYC_guide1,MYC,GTACTTGGTGAGGCCAGCGC
non-targeting_1,control,GTAGCGAACGTGTCCGGCGT

Documentation

• Installation
• Quick Start Tutorial
• Complete Workflow
• Scanpy Integration Guide
• CLI Examples
• All Examples

Requirements

• Python 3.9+
• AnnData/Scanpy for single-cell analysis
• Works on macOS, Linux, and Windows

Authors

This work was developed by Siavash Ghaffari. For any questions, feedback, or additional information, please feel free to reach out. Your input is highly valued and will help improve and refine this pipeline further.