Data & ReproSingle-Cell & Spatial OmicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-single-cell-perturb-seq

Maintainer FreedomIntelligence · Last updated April 1, 2026

Analyze Perturb-seq and CROP-seq CRISPR screening data integrated with scRNA-seq. Use when identifying gene function through pooled genetic perturbations in single cells.

OpenClawNanoClawAnalysisReproductionbio-single-cell-perturb-seq🧬 bioinformatics (gptomics bio-* suite)bioinformatics — single-cell & spatial omicsanalyze

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-single-cell-perturb-seq

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

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

Python: pertpy.tl.Mixscape(adata) for perturbation classification, pertpy.tl.Augur for prioritization.
Analyze my Perturb-seq CRISPR screen" → Link guide RNA assignments to transcriptional phenotypes in pooled CRISPR screens with single-cell readout to identify gene function. Python: pertpy.tl.Mixscape(adata) for perturbation classification, pertpy.tl.Augur for prioritization.
adata.obs['guide_id'] = guide_assignments['guide_id'] adata.obs['target_gene'] = guide_assignments['target_gene'].

Source Doc

Excerpt From SKILL.md

Load and Annotate Perturbations

import scanpy as sc
import pertpy as pt

adata = sc.read_h5ad('perturb_seq.h5ad')

## Mark non-targeting controls

adata.obs['is_control'] = adata.obs['target_gene'] == 'non-targeting'

Initialize perturbation analysis

ps = pt.tl.PerturbationSpace(adata)

Use cases

Use when identifying gene function through pooled genetic perturbations in single cells.

Not for

Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

single-cell/preprocessing - scRNA-seq preprocessing
single-cell/markers-annotation - DE and marker gene concepts
single-cell/batch-integration - Multi-sample integration
crispr-screens/mageck-analysis - Bulk screen analysis

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