feat: mcp

[mtran-code]

Work done for PGx agent

[coderabbitai]

Important

Review skipped

Too many files!

This PR contains 131 files, which is 31 over the limit of 100.

To get a review, reduce the PR to 100 files or fewer by splitting it into smaller PRs or changing its base branch.

Upgrade to a paid plan to raise the limit.

This review couldn't start because sufficient usage credits or metered capacity aren't available. Add credits or update usage-based reviews in the billing tab, then retry.

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro Plus

Run ID: 35c7000d-6e11-4aa8-8450-429d8c64ff9d

📥 Commits

Reviewing files that changed from the base of the PR and between 5bf2268 and 28c5870.

📒 Files selected for processing (131)

• .github/workflows/check-bioc.yml
• .gitignore
• DESCRIPTION
• Dockerfile
• NAMESPACE
• NEWS.md
• R/GR.R
• R/GWC.R
• R/PharmacoSet-accessors.R
• R/PharmacoSet-class.R
• R/PharmacoSet-utils.R
• R/adaptiveMatthewCor.R
• R/callingWaterfall.R
• R/class-SignatureClass.R
• R/computeABC.R
• R/computeAUC.R
• R/computeAUC_old.R
• R/computeAmax.R
• R/computeDSS.R
• R/computeDrugSensitivity.R
• R/computeGR.R
• R/computeIC50.R
• R/computeICn.R
• R/computeSlope.R
• R/computeSynergy.R
• R/connectivityScore.R
• R/cosinePerm.R
• R/curveFittingPGX.R
• R/datasets.R
• R/downloadPSet.R
• R/downloadSignatures.R
• R/drugDoseResponseCurve.R
• R/drugPerturbationSig.R
• R/filterNoisyCurves.R
• R/geneDrugPerturbation.R
• R/geneDrugSensitivity.R
• R/geneDrugSensitivityPBCorr.R
• R/geneDrugSensitivityPCorr.R
• R/getRawSensitivityMatrix.R
• R/globals.R
• R/intersectPSets.R
• R/logLogisticRegression.R
• R/matthewCor.R
• R/mergePSets.R
• R/methods-[.R
• R/methods-drugSensitivitySig.R
• R/methods-intersect.R
• R/methods-subsetTo.R
• R/methods-summarizeMolecularProfiles.R
• R/methods-summarizeSensitivityProfiles.R
• R/plotPSig.R
• R/rankGeneDrugPerturbation.R
• R/rankGeneDrugSensitivity.R
• R/sanityCheck.R
• R/updateObject-methods.R
• R/zzz.R
• README.md
• codecover.R
• inst/mcp/PharmacoGx-tools.R
• inst/mcp/README.md
• inst/mcp/biomni-mcp-config.yaml
• inst/mcp/manuscript-architecture.md
• inst/mcp/run-pharmacogx-mcp.R
• inst/mcp/tooluniverse-mcp-tools-config.json
• inst/skills/pharmacogx-agentic-analysis/SKILL.md
• man/CCLEsmall.Rd
• man/CMAPsmall.Rd
• man/GDSCsmall.Rd
• man/PharmacoSet-accessors.Rd
• man/PharmacoSet-class.Rd
• man/PharmacoSet2.Rd
• man/computeAUC.Rd
• man/computeAmax.Rd
• man/computeHSA.Rd
• man/computeICn.Rd
• man/computeLoewe.Rd
• man/computeSlope.Rd
• man/computeZIPdelta-TreatmentResponseExperiment-method.Rd
• man/cosinePerm.Rd
• man/curveFittingPGX.Rd
• man/dot-computeZIPdelta.Rd
• man/dot-normalizeBiphasicPars.Rd
• man/dot-normalizeHillPars.Rd
• man/dot-pgx_biphasic_curve.Rd
• man/dot-pgx_hill_curve.Rd
• man/dot-summarizeSensProfiles.Rd
• man/downloadPSet.Rd
• man/downloadPertSig.Rd
• man/drugDoseResponseCurve.Rd
• man/drugSensitivitySig-PharmacoSet-method.Rd
• man/effectToDose.Rd
• man/filterNoisyCurves.Rd
• man/fitTwowayZIP.Rd
• man/hillCurve.Rd
• man/intersectPSet.Rd
• man/loeweCI.Rd
• man/logLogisticRegression.Rd
• man/mcc.Rd
• man/plot.PharmacoSig.Rd
• man/summarizeMolecularProfiles-PharmacoSet-method.Rd
• man/summarizeSensitivityProfiles-PharmacoSet-method.Rd
• tests/testthat/test_Hill.R
• tests/testthat/test_PharmacoSetClass.R
• tests/testthat/test_PharmacoSet_utils.R
• tests/testthat/test_bracket_pharmacoset.R
• tests/testthat/test_computeABC.R
• tests/testthat/test_computeAUC.R
• tests/testthat/test_computeAmax.R
• tests/testthat/test_computeDSS.R
• tests/testthat/test_computeHSA.R
• tests/testthat/test_computeIC50.R
• tests/testthat/test_computeSlope.R
• tests/testthat/test_computeZIPdelta.R
• tests/testthat/test_downloadPSet.R
• tests/testthat/test_drugDoseResponseCurve.R
• tests/testthat/test_drugPerturbationSig.R
• tests/testthat/test_drugSensitivitySig.R
• tests/testthat/test_intersectPSet.R
• tests/testthat/test_logLogisticRegression.R
• tests/testthat/test_sanitizeInput.R
• tests/testthat/test_subsetTo.R
• tests/testthat/test_summarizeMolecularProfiles.R
• tests/testthat/test_summarizeMolecularProfiles_missing_ucell.R
• tests/testthat/test_summarizeSensitivityProfiles.R
• tests/testthat/test_summarizeSensitivityProfiles_longtable.R
• tests/testthat/test_unionList.R
• vignettes/CreatingPharmacoSet.Rmd
• vignettes/DetectingDrugSynergyAndAntagonism.R
• vignettes/DetectingDrugSynergyAndAntagonism.Rmd
• vignettes/PharmacoGx.Rmd
• vignettes/pharmacogx.bib

You can disable this status message by setting the reviews.review_status to false in the CodeRabbit configuration file.

---

Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out.

❤️ Share

• X
• Mastodon
• Reddit
• LinkedIn

_{Comment @coderabbitai help to get the list of available commands.}