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数据与复现药物发现与化学信息学K-Dense-AI/claude-scientific-skills数据与复现
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depmap

维护者 Kuan-lin Huang · 最近更新 2026年4月1日

The Cancer Dependency Map (DepMap) project, run by the Broad Institute, systematically characteri.

Claude CodeOpenClawNanoClaw分析处理复现实验depmapchemistrypackagecheminformatics & drug discovery

原始来源

K-Dense-AI/claude-scientific-skills

https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/depmap

维护者
Kuan-lin Huang
许可
CC-BY-4.0
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

  • Identifying which genes are essential ，用于 specific cancer types。
  • Finding cancer-selective dependencies (therapeutic targets)。
  • Validating oncology drug targets。
  • Discovering synthetic lethal interactions。
  • DepMap Portal：https：//depmap.org/portal/。

原始文档

SKILL.md 摘录

When to Use This Skill

Use DepMap when:

  • Target validation: Is a gene essential for survival in cancer cell lines with a specific mutation (e.g., KRAS-mutant)?
  • Biomarker discovery: What genomic features predict sensitivity to knockout of a gene?
  • Synthetic lethality: Find genes that are selectively essential when another gene is mutated/deleted
  • Drug sensitivity: What cell line features predict response to a compound?
  • Pan-cancer essentiality: Is a gene broadly essential across all cancer types (bad target) or selectively essential?
  • Correlation analysis: Which pairs of genes have correlated dependency profiles (co-essentiality)?

Dependency Scores

ScoreRangeMeaning
Chronos (CRISPR)~ -3 to 0+More negative = more essential. Common essential threshold: −1. Pan-essential genes ~−1 to −2
RNAi DEMETER2~ -3 to 0+Similar scale to Chronos
Gene EffectnormalizedNormalized Chronos; −1 = median effect of common essential genes

Key thresholds:

  • Chronos ≤ −0.5: likely dependent
  • Chronos ≤ −1: strongly dependent (common essential range)

Cell Line Annotations

Each cell line has:

  • DepMap_ID: unique identifier (e.g., ACH-000001)
  • cell_line_name: human-readable name
  • primary_disease: cancer type
  • lineage: broad tissue lineage
  • lineage_subtype: specific subtype

适用场景

  • **Target validation**：Is gene essential ，用于 survival in cancer cell lines ，支持 specific mutation (e.g.，KRAS-mutant)。
  • **Biomarker discovery**：What genomic features predict sensitivity to knockout of gene。
  • **Synthetic lethality**：Find genes that are selectively essential when another gene is mutated/deleted。
  • **Drug sensitivity**：What cell line features predict response to compound。

不适用场景

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

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