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bio-single-cell-perturb-seq

维护者 FreedomIntelligence · 最近更新 2026年4月1日

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.

OpenClawNanoClaw分析处理复现实验bio-single-cell-perturb-seq🧬 bioinformatics (gptomics bio-* suite)bioinformatics — single-cell & spatial omicsanalyze

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

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

维护者
FreedomIntelligence
许可
MIT
最近更新
2026年4月1日

技能摘要

来自 SKILL.md 的关键信息

2 min

核心说明

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

原始文档

SKILL.md 摘录

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)

适用场景

  • 适合在identifying gene function through pooled genetic perturbations in single cells时使用。

不适用场景

  • Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。

上游相关技能

  • 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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