All recipes

Every catalogued recipe, one page each. Use the sidebar (or the search box at the top of the page) to jump to a specific recipe. To browse by problem class or see where the gaps are, see the Landscape. To return to the section overview, see Recipes.

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Table of contents

• Analyze an existing MD trajectory for stability, flexibility, and contacts - Drive the MDAnalysis skill (MDTraj as backup) to take a finished GROMACS/AMBER/NAMD trajectory through RMSD/RMSF/Rg, contact maps, H-bonds, and PCA without writing the analysis script by hand.
• Assemble a tissue reference atlas from the CELLxGENE Census - Use the cellxgene-census Claude skill to slice a tissue- or disease-specific AnnData from the CZ CELLxGENE Census, optionally fetching the precomputed scVI embedding for reference mapping or downstream integration.
• Benchmark an ADMET property with PyTDC - Drive the PyTDC Claude skill to load a Therapeutics Data Commons ADMET dataset with its leaderboard split, train or score a baseline model, and emit the standard TDC metrics so a new method can be compared head-to-head against the leaderboard.
• Build a pharmacogenomic dosing report from a patient's diplotypes - Turn a patient's PGx diplotypes plus a medication list into CPIC/DPWG genotype-to-dosing recommendations with cited guideline sources.
• Build a phylogenetic tree from a set of sequences - Use the phylogenetics Claude skill to take a FASTA of homologous sequences through MAFFT alignment, IQ-TREE 2 maximum-likelihood inference with bootstrap support, and an annotated tree figure.
• Build a target dossier from gene name to structure to cancer dependency - Combine the Open Targets plugin, UniProt MCP, AlphaFold MCP, and the DepMap skill to produce a one-page dossier on a candidate gene — disease evidence, protein annotation, predicted structure, and cancer-cell-line essentiality.
• Call peaks and find enriched motifs from ChIP-seq or ATAC-seq - Chain the MACS3 peak-calling skill into the HOMER motif skill to turn aligned ChIP-seq/ATAC-seq BAMs into a called-peak set with nearest-gene annotation and enriched TF motifs.
• Compute 16S microbiome alpha/beta diversity from a BIOM table - Use the scikit-bio Claude skill to take a BIOM feature table and sample metadata through Shannon/Simpson/Faith's PD, UniFrac, PCoA, and PERMANOVA in one chat.
• Compute a bacterial pan-genome from a set of genome assemblies - Annotate a panel of bacterial assemblies with Bakta, then cluster genes into core/accessory partitions with Roary to get a pan-genome and presence/absence matrix.
• Compute HRV from an ECG recording - Use the NeuroKit2 Claude Skill to clean an ECG trace, detect R-peaks, and return time-domain, frequency-domain, and non-linear HRV indices from a single conversation.
• Convert raw analytical instrument data to Allotrope ASM JSON - Drop a raw instrument file (cell counter, plate reader, HPLC, qPCR) onto Claude Code and get back valid Allotrope Simple Model JSON, a flattened CSV for LIMS, and a standalone Python parser script.
• Discover NWB recordings on DANDI and prepare them for sorting - Use the Neurosift Tools MCP to find Neuropixels (or other extracellular) NWB sessions on DANDI matching your hypothesis, inspect them in-place, and stage a download list for downstream spike sorting.
• Dock a ligand library into a target structure with DiffDock - Drive DiffDock from Claude Code to generate per-ligand binding poses against a PDB or AlphaFold target, filter by confidence, and emit a ranked pose set ready for MM/PBSA rescoring or visualization.
• Draft a Phase 2/3 clinical-trial protocol from an indication brief - Use the Anthropic clinical-trial-protocol plugin to expand a short indication / endpoint brief into an FDA/NIH-compliant Phase 2/3 protocol draft, with regulatory pathway, competitive landscape, and sample-size calculation already wired in.
• Enumerate analogs around a lead compound for SAR expansion - Use the Datamol skill in Claude Code to enumerate standardized, drug-like analogs around a lead SMILES — tautomers, stereoisomers, and fragment-substituted variants — as a ranked SAR-expansion table.
• Estimate pharmacokinetic properties of a small molecule - Combine RDKit physchem descriptors, MedChem rule-based ADMET flags, and measured ChEMBL bioactivity / DMPK endpoints to build a defensible PK estimate for one compound without an ML predictor in the loop.
• Filter a virtual screening hit list with drug-likeness rules and structural alerts - Use the MedChem skill in Claude Code to cascade Lipinski / Veber / PAINS / BRENK filters over a SMILES hit list and emit a triaged CSV with per-rule flags and a final keep/drop column.
• Identify an unknown compound from an MS/MS spectrum - Use the matchms skill in Claude Code to clean an unknown MS/MS spectrum and rank candidate identities by spectral similarity against a reference library.
• Infer cell-cell communication from single-cell RNA-seq - Use the LIANA-MCP server to run multiple ligand-receptor methods on an annotated AnnData object, aggregate their ranks, and plot the consensus communication network.
• Infer a gene-regulatory network from single-cell RNA-seq - Use the Arboreto Claude skill to run GRNBoost2 on a QC'd single-cell AnnData and recover a ranked TF–target edge list — the first step of a SCENIC regulon pipeline.
• Integrate multiple single-cell RNA-seq datasets across batches - Use the scvi-tools skill in Claude Code to fit scVI (or scANVI when labels are available) on a concatenated AnnData of multiple batches, returning a batch-corrected latent space and integrated UMAP.
• Interpret a clinical variant from a natural-language query - Use BioMCP to convert a free-text variant query ("BRAF V600E", "rs113993960", "NM_004985.5:c.35G>A") into a one-page clinical report with ClinVar significance, population frequency, in-silico predictions, and linked literature.
• Match a patient summary to recruiting clinical trials - Use BioMCP (or the standalone ClinicalTrials.gov MCP) to take a free-text patient summary and return a ranked list of currently-recruiting trials with eligibility rationale.
• Organize a raw DICOM dataset into a BIDS layout - Drive HeuDiConv or dcm2bids from Claude Code via the K-Dense BIDS skill to convert a raw DICOM dump into a validated BIDS dataset ready for BIDS-Apps and OpenNeuro submission.
• Parse FCS flow-cytometry files for downstream immunophenotyping - Use the FlowIO Claude skill to parse FCS 2.0/3.0/3.1 files into tidy DataFrames with channel categorisation and batch metadata extraction, ready for downstream immunophenotyping or QC.
• Predict gene-knockout phenotypes with flux balance analysis - Use the COBRApy Claude Skill to load a genome-scale metabolic model and screen single/double gene deletions for growth phenotypes and essential genes.
• Prioritize targets within a disease via Open Targets - Drive the Open Targets MCP plugin to rank candidate targets within a disease across the four prioritisation pillars (precedence, tractability, doability, safety) and emit a cited target shortlist.
• Profile a cancer cohort's genomics with cBioPortal - Use the cBioPortal Claude Skill to query TCGA-scale studies for mutation frequency, oncoprints, TMB, and survival by genomic subgroup in plain language.
• Profile ChIP-seq or ATAC-seq signal around genomic features - Use the deepTools Claude Skill to turn aligned ChIP-seq/ATAC-seq BAMs into normalized bigWig tracks and TSS/peak-centered profile and heatmap figures.
• Profile a compound's polypharmacology from ChEMBL bioactivity data - Use the ChEMBL connector in Claude Code to pull every measured activity for one compound, group by target and assay, and surface the off-target profile a medicinal chemist needs before committing to a chemotype.
• Run bulk RNA-seq differential expression from a counts matrix - Use the PyDESeq2 Claude Skill to fit a negative-binomial GLM from a counts matrix and sample-condition table, returning ranked log2 fold-change and BH-adjusted p-values.
• Run first-pass QC on a single-cell RNA-seq dataset - Use Anthropic's single-cell-rna-qc skill to MAD-filter a 10x .h5 or AnnData .h5ad file and emit standard QC figures before downstream Scanpy or scvi-tools work.
• Run functional enrichment on a gene list - Use the gget Claude skill to run a gene list through Enrichr against GO, KEGG, Reactome, and disease libraries, then ask Claude to summarise the enriched terms back to the biology with explicit citations.
• Run a GWAS on case-control genotype data - Drive PLINK2 from QC through PCA-adjusted logistic-regression association on a case-control cohort, returning Manhattan-ready summary stats.
• Scan a therapeutic antibody for glycosylation sites - Use the Glycoengineering skill to scan an antibody sequence for N-glycosylation sequons and O-glycosylation hotspots before committing to a cell-line or developability campaign.
• Scan approved drugs for repurposing candidates against a disease - Given a disease, use Open Targets to rank associated targets, ChEMBL and PubChem for approved-drug bioactivity, and DrugBank for mechanism / indication / interaction context to produce a ranked shortlist of repurposing candidates.
• Screen a polypharmacy medication list for drug-drug interactions - Ground Claude in the DDInter skill to screen a multi-drug medication list for pairwise interactions with severity and mechanism, instead of asking the model from memory.
• Set up a protein molecular dynamics simulation in GROMACS from a PDB ID - Drive the GROMACS Copilot component of molecule-mcp to take a PDB ID through topology, solvation, ion neutralisation, minimisation, NVT/NPT equilibration, and a short production MD, with RMSD/RMSF/Rg analysis on the resulting trajectory.
• Sort spikes from a Neuropixels recording end-to-end - Use the K-Dense neuropixels-analysis skill in Claude Code to take a raw SpikeGLX or Open Ephys Neuropixels recording through preprocessing, drift correction, and Kilosort4 to curated single units.
• Triage a stack of new preprints in your field - Use the bio-research plugin in Claude Code to pull last-week bioRxiv and PubMed hits, rank by relevance, and produce a one-paragraph readout per paper.
• Triage an AlphaFold model for structure-based drug design - Pull a UniProt AlphaFold prediction, surface pLDDT regions and pocket-residue confidence, and produce a go/no-go verdict on whether the model is fit for downstream docking or modelling — all from one MCP server.
• Fit a survival model to censored clinical outcomes - Use the scikit-survival Claude Skill to fit Cox and Random Survival Forest models to censored time-to-event data and report concordance with proper validation.
• Scan adverse-event reports for a drug-safety signal - Use the OpenFDA MCP server to pull FAERS adverse-event reports and label warnings for a drug, rank the top reported reactions, and assemble a pharmacovigilance snapshot.
• Score point mutations for functional impact with a protein language model - Use the ESM skill to compute zero-shot masked-marginal log-likelihood-ratio scores for a list of point mutations, ranking them by predicted functional effect without any labelled data.