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Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles.
Passed 21 of 21 test cases with the skill, and 17 of 21 without it.
and 2 more in the full report
4 fixed18 passed either way0 still failing0 broke
Tokens, turns and time describe resource use, not a dollar price.
One of 3 test cases the skill fixed. Same model, same prompt, with and without the skill.
Write a Python function for DepMap biomarker evaluation that tests if loss-of-function mutation in ARID1A predicts increased dependency on ARID1B. Using a gene effect DataFrame and a binary mutation matrix DataFrame, compare the score distributions of ARID1A-mutated versus wild-type lines, and yield a summary dictionary detailing the count of mutated lines, count of WT lines, mean score of each group, calculated p-value, and whether the association is statistically significant.
| Checked | Without skill | With skill |
|---|---|---|
| The function performs a Mann-Whitney U statistical test on the dependency scores. | Missed | Passed |
| The statistical test specifies alternative='less' for the hypothesis direction. | Missed | Passed |
The instructions your model reads when the skill loads.
-|-------|---------| | 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 Effect | normalized | Normalized Chronos; −1 = median effect of common essential genes |
Key thresholds:
Each cell line has:
DepMap_ID: unique identifier (e.g., ACH-000001)cell_line_name: human-readable nameprimary_disease: cancer typelineage: broad tissue lineagelineage_subtype: specific subtypeimport requests
import pandas as pd
BASE_URL = "https://depmap.org/portal/api"
def depmap_get(endpoint, params=None):
url = f"{BASE_URL}/{endpoint}"
response = requests.get(url, params=params)
response.raise_for_status()
return response.json()
def get_gene_dependency(gene_symbol, dataset="Chronos_Combined"):
"""Get CRISPR dependency scores for a gene across all cell lines."""
test cases passed, vs 17 / 21 without
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