数据与复现统计与数据分析FreedomIntelligence/OpenClaw-Medical-Skills数据与复现

bio-crispr-screens-hit-calling

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

bio-crispr-screens-hit-calling：Statistical methods ，用于 calling hits in CRISPR screens。 Covers MAGeCK，BAGEL2，drugZ，、 custom approaches ，用于 identifying essential 、 resistance genes。适合在identifying significant genes ，面向 screen count data after QC passes时使用。

OpenClawNanoClaw分析处理复现实验bio-crispr-screens-hit-calling🧬 bioinformatics (gptomics bio-* suite)bioinformatics — epidemiological & causal genomicsstatistical

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-crispr-screens-hit-calling

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

CLI：BAGEL.py bf ，用于 Bayes factor essentiality scoring。
Python：drugZ ，用于 fold-change based analysis。
Identify essential genes ，面向 my CRISPR screen" → Call significant gene hits ，面向 sgRNA count data ，使用 statistical methods that account ，用于 guide-level variability 、 multiple testing. CLI：BAGEL.py bf ，用于 Bayes factor essentiality scoring Python：drugZ ，用于 fold-change based analysis。
bagel2 fc \ -i counts.txt \ -o foldchange.txt \ -c Control1，Control2 \ -t Treatment1，Treatment2。

原始文档

SKILL.md 摘录

BAGEL2 Analysis

Goal: Identify essential genes using Bayesian classification against reference gene sets.

Approach: Calculate sgRNA fold changes, compute Bayes Factors using known essential and non-essential gene sets as training data, and assess precision-recall at different thresholds.


## Calculate Bayes Factor

bagel2 bf \
    -i foldchange.txt \
    -o bayes_factor.txt \
    -e essential_genes.txt \
    -n nonessential_genes.txt \
    -c 1  # Number of bootstrap iterations

## Precision-recall analysis

bagel2 pr \
    -i bayes_factor.txt \
    -o precision_recall.txt \
    -e essential_genes.txt \
    -n nonessential_genes.txt

适用场景

适合在identifying significant genes ，面向 screen count data after QC passes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

mageck-analysis - MAGeCK workflow
screen-qc - QC before hit calling
pathway-analysis/go-enrichment - Functional analysis of hits

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