Agent skills for healthcare and life sciences: genomics, imaging, claims, drug discovery, and more. Works with Amazon Quick, Kiro, Amazon AgentCore, AWS Strands SDK, Claude Code, Codex, and any Agent Skills-compatible platform.
awslabs/hcls-agent-skills is a collection of reusable instructions that help AI agents handle healthcare and life sciences work, including genomics, medical imaging, claims, and drug discovery. It is intended for agents running on Agent Skills-compatible platforms, and the catalogue entries are its individual domain skills.
Skill Claude CodeCodex ✓ vendor
Reason about pharmacoepidemiologic study design for causal inference from real-world data — choosing active comparator new-user designs, emulating target trials, avoiding immortal time bias, handling time-varying confounding with marginal structural models, and selecting propensity score methods. Use when the user…
Skill Claude CodeCodex ✓ vendor
Pipeline skill for protein structure analysis covering PDB/mmCIF parsing, RMSD superposition, Ramachandran/dihedral analysis, binding pocket detection, contact maps, B-factor flexibility, DSSP secondary structure, and format conversion. Triggers on PDB, protein structure, RMSD, Ramachandran, binding pocket, Biopython…
Skill Claude CodeCodex ✓ vendor
Reasoning skill for healthcare revenue cycle denial management. Use when the user needs to appeal a claim denial, draft a payer-ready denial appeal letter, analyze a denial reason code, or determine whether a denied claim should be overturned, pended, or accepted. Triggers include "appeal a claim denial", "draft…
Skill Claude CodeCodex ✓ vendor
Pipeline skill for computing HEDIS quality measures from claims and clinical data. Use when the user asks to calculate HEDIS measure rates, check continuous enrollment, build denominator/numerator logic, detect care gaps, compute utilization rates, identify high-cost claimants, or score risk stratification indices.…
Skill Claude CodeCodex ✓ vendor
Reason about quantitative proteomics experiment design and data analysis strategy. Use when the user asks to choose between LFQ, TMT, and DIA quantification; select an imputation method for missing values; pick a normalization strategy; interpret differential expression results from proteomics data; evaluate ratio…
Skill Claude CodeCodex ✓ vendor
Structural MRI/CT preprocessing pipeline for radiology workflows covering skull stripping, bias field correction, registration, and intensity normalization. Triggers on skull stripping, bias correction, registration, ANTs, FSL, HD-BET, N4, brain extraction, normalization, FLIRT, FNIRT, SyN, fslreorient2std, MNI…
Skill Claude CodeCodex ✓ vendor
Reasoning skill for CMS-HCC risk adjustment strategy and methodology. Use when the user asks about CMS-HCC model versions V24 or V28, blended transition methodology, ICD-10-to-HCC mapping logic, disease interaction hierarchies, RAF score methodology, risk adjustment factor calculation, coding gap identification…
Skill Claude CodeCodex ✓ vendor
Pipeline skill for CMS-HCC risk adjustment calculation and coding gap identification. Use when the user asks to apply the ICD-10-to-HCC crosswalk, calculate RAF scores, resolve disease hierarchies programmatically, identify coding gaps from Rx or lab proxies, project member-level risk scores, build a risk adjustment…
Skill Claude CodeCodex ✓ vendor
Reasoning skill for clinical risk stratification index selection and interpretation. Use when the user asks about LACE scores, Charlson Comorbidity Index, Elixhauser Index, readmission risk scoring, comorbidity weighting, SDOH Z-codes, Area Deprivation Index, or population health stratification methods.
Skill Claude CodeCodex ✓ vendor
Bulk RNA-seq analysis pipeline covering alignment (STAR), quantification (Salmon, featureCounts), and differential expression (DESeq2). Triggers on RNA-seq, STAR, Salmon, DESeq2, differential expression, gene expression, tximport, featureCounts, transcriptomics, "bulk RNA-seq", "STAR alignment", "Salmon…
Skill Claude CodeCodex ✓ vendor
Real-world data cohort analysis pipeline for claims and EHR data — cohort identification with ICD-10, NDC, and CPT codes, medication adherence metrics (PDC/MPR), propensity score estimation and balance diagnostics, Kaplan-Meier survival curves, and Cox proportional hazards models. Use when the user mentions claims…
Skill Claude CodeCodex ✓ vendor
Scanpy-based single-cell RNA-seq analysis pipeline covering loading (10X, h5ad), QC, normalization, HVG selection, PCA/UMAP, Leiden clustering, differential expression, and batch correction (Harmony, scVI). Use when the user mentions single-cell, scRNA-seq, Scanpy, AnnData, UMAP, clustering, 10X, h5ad, leiden, highly…
Skill Claude CodeCodex ✓ vendor
Reasoning skill for structure-based drug design strategy. Use when the user asks to assess target druggability, choose a docking strategy, select a scoring function, define a binding site, interpret docking results, plan molecular dynamics or free energy perturbation (FEP), design a virtual screening cascade, or…
Skill Claude CodeCodex ✓ vendor
Single-cell trajectory inference pipeline covering diffusion pseudotime (DPT), PAGA, RNA velocity with scVelo, and fate mapping with CellRank. Use when the user mentions pseudotime, trajectory, lineage, differentiation, RNA velocity, scVelo, CellRank, PAGA, diffusion map, fate probabilities, terminal states…
Skill Claude CodeCodex ✓ vendor
Reason about translational research problems in HCLS — especially neurology and hypothesis validation. Use when the user asks to design a validation study, evaluate a target, qualify a biomarker, choose endpoints, critique a preclinical-to-clinical plan, pick a trial design (basket/umbrella/platform), plan multimodal…
Skill Claude CodeCodex ✓ vendor
Germline and somatic short-variant calling pipeline for Illumina short-read data. Use when the user mentions BWA, BWA-MEM2, GATK, HaplotypeCaller, Mutect2, VCF, GVCF, VQSR, variant calling, germline, somatic, SNV, or indel calling from FASTQ/BAM.
Skill Claude CodeCodex ✓ vendor
Reasoning skill for Coordination of Benefits (COB) determination in healthcare claims. Use when a claim involves multiple insurers and the user needs to know which plan pays first, how to sequence billing, or why a COB-related denial or underpayment occurred. Covers Medicare Secondary Payer (MSP) rules and NAIC…
At most 3 mods per repository are shown here, and a mod shipped inside a plugin is left to that plugin's page — the rest are on their repository pages: