drug-response

Drug Response

Dose-response modeling and drug sensitivity prediction in cancer cell lines. Covers IC50 and AUC estimation from viability curves, retrieval and harmonization of GDSC, CTRP, and PRISM data through PharmacoGx, DepMap dependency and drug data, sensitivity prediction with regularized regression, and pharmacogenomic biomarker discovery.

When to Use This Skill

Activate when the user requests:

• IC50, EC50, or AUC estimation from dose-response data
• Four-parameter logistic (4PL) curve fitting
• GDSC, CTRP, PRISM, or CCLE drug sensitivity retrieval
• DepMap dependency or drug screen data
• Cross-dataset harmonization of drug response
• Drug sensitivity prediction from expression or mutation
• Pharmacogenomic biomarker discovery
• Distinguishing IC50 from AUC as a response metric

Inputs

Data Type	Format	Source
Dose-response	Concentration, viability per well	Screening plates, published curves
Curated sensitivity	PharmacoSet (.rds)	PharmacoGx, ORCESTRA
Cell line molecular	Expression, mutation, CNV matrices	DepMap, CCLE
Drug annotation	SMILES, target, mechanism	DepMap, ChEMBL

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Environment

Versions verified 2026-08.

# Curated drug response, the practical entry point
BiocManager::install("PharmacoGx")      # 3.16.0 (Bioconductor)
#   NOT the CRAN PharmacoGx, which is frozen at 1.1.6 from 2016.
#   install.packages("PharmacoGx") gets a decade-old package. Use Bioconductor.

# Dose-response curve fitting
install.packages("drc")                 # 3.0-1 (2016). Stale but standard.
install.packages("nplr")                # 0.1-8 (2025). Maintained alternative.

# GDSC's own fitting pipeline
# remotes::install_github("CancerRxGene/gdscIC50")   # not on CRAN

# DepMap data in R
BiocManager::install("depmap")          # ExperimentHub interface to releases

Data source status, checked 2026-08:

  DepMap            depmap.org/portal — up. Distributes CCLE molecular data,
                    CRISPR dependency (Chronos), and the PRISM drug repurposing
                    screen. The practical download host.
  cancerrxgene.org  the GDSC website is currently returning HTTP 410 Gone,
                    on every path. Do not hardcode a download URL against it.
                    GDSC processed data is mirrored through DepMap and wrapped
                    by PharmacoGx, which is how to obtain it reliably now.
  PharmacoDB        pharmacodb.ca — up. Cross-dataset query interface.
  ORCESTRA          orcestra.ca — versioned, citable PharmacoSet objects.

Because the primary GDSC portal is unstable, prefer the curated PharmacoSet
route over scraping raw files. It also fixes the harmonization problems below.